Package 'CRBHits'

aa2rbh

Description

This function calculates (conditional-)reciprocal best hit (CRBHit) pairs from two AA AAStringSet's. Conditional-reciprocal best hit pairs were introduced by Aubry S, Kelly S et al. (2014). Sequence searches are performed with last Kiełbasa, SM et al. (2011) [default] or with mmseqs2 Steinegger, M and Soeding, J (2017) or with diamond Buchfink, B et al. (2021). If one specifies aa1 and aa2 as the same input a selfblast is conducted.

Usage

aa2rbh(
  aa1,
  aa2,
  dbfile1 = NULL,
  dbfile2 = NULL,
  searchtool = "last",
  lastpath = file.path(find.package("CRBHits"), "extdata", "last-1639", "bin"),
  lastD = 1e+06,
  lastm = 10,
  mmseqs2path = NULL,
  mmseqs2sensitivity = 5.7,
  mmseqs2maxseqs = 300,
  diamondpath = NULL,
  diamondsensitivity = "--sensitive",
  diamondmaxtargetseqs = 0,
  lambda3path = NULL,
  lambda3sensitivity = "sensitive",
  lambda3nummatches = 25,
  outpath = "/tmp",
  crbh = TRUE,
  keepSingleDirection = FALSE,
  eval = 0.001,
  qcov = 0,
  tcov = 0,
  pident = 0,
  alnlen = 0,
  rost1999 = FALSE,
  filter = NULL,
  plotCurve = FALSE,
  fit.type = "mean",
  fit.varweight = 0.1,
  fit.min = 5,
  threads = 1,
  remove = TRUE,
  remove.db = TRUE
)

Arguments

aa1	aa1 sequences as AAStringSet [mandatory]
aa2	aa2 sequences as AAStringSet [mandatory]
dbfile1	aa1 db file [optional]
dbfile2	aa2 db file [optional]
searchtool	specify sequence search algorithm last, mmseqs2, diamond or lambda3 [default: last]
lastpath	specify the PATH to the last binaries [default: /extdata/last-1639/bin/]
lastD	last option D: query letters per random alignment [default: 1e6]
lastm	last option m: maximum initial matches per query position [default: 10]
mmseqs2path	specify the PATH to the mmseqs2 binaries [default: NULL]
mmseqs2sensitivity	specify the sensitivity option of mmseqs2 [default: 5.7]
mmseqs2maxseqs	mmseqs2 option: Maximum results per query sequence allowed to pass the prefilter [default: 300]
diamondpath	specify the PATH to the diamond binaries [default: NULL]
diamondsensitivity	specify the sensitivity option of diamond [default: –sensitive]
diamondmaxtargetseqs	specify the maximum number of target sequences per query option of diamond [default: 0]
lambda3path	specify the PATH to the lambda3 binaries [default: NULL]
lambda3sensitivity	specify the sensitivity option of lambda3 [default: sensitive]
lambda3nummatches	specify the number of matches per query option of lambda3 [default: 25]
outpath	specify the output PATH [default: /tmp]
crbh	specify if conditional-reciprocal hit pairs should be retained as secondary hits [default: TRUE]
keepSingleDirection	specify if single direction secondary hit pairs should be retained [default: FALSE]
eval	evalue [default: 1e-3]
qcov	query coverage [default: 0.0]
tcov	target coverage [default: 0.0]
pident	percent identity [default: 0.0]
alnlen	alignment length [default: 0.0]
rost1999	specify if hit pairs should be filter by equation 2 of Rost 1999 [default: FALSE]
filter	specify additional custom filters as list to be applied on hit pairs [default: NULL]
plotCurve	specify if crbh fitting curve should be plotted [default: FALSE]
fit.type	specify if mean or median should be used for fitting [default: mean]
fit.varweight	factor for fitting function to consider neighborhood [default: 0.1]
fit.min	specify minimum neighborhood alignment length [default: 5]
threads	number of parallel threads [default: 1]
remove	specify if last result files should be removed [default: TRUE]
remove.db	specify if last db files should be removed [default: TRUE]

Value

List of three (crbh=FALSE)
1: $crbh.pairs
2: $crbh1 matrix; query > target
3: $crbh2 matrix; target > query

List of four (crbh=TRUE)
1: $crbh.pairs
2: $crbh1 matrix; query > target
3: $crbh2 matrix; target > query
4: $rbh1_rbh2_fit; evalue fitting function

Author(s)

Kristian K Ullrich

References

Aubry S, Kelly S et al. (2014) Deep Evolutionary Comparison of Gene Expression Identifies Parallel Recruitment of Trans-Factors in Two Independent Origins of C4 Photosynthesis. PLOS Genetics, 10(6) e1004365.

Kiełbasa, SM et al. (2011) Adaptive seeds tame genomic sequence comparison. Genome research, 21(3), 487-493.

Rost B. (1999). Twilight zone of protein sequence alignments. Protein Engineering, 12(2), 85-94.

See Also

cds2rbh

Examples

## compile last-1639 within CRBHits
CRBHits::make_last()
## load example sequence data
data("ath", package="CRBHits")
data("aly", package="CRBHits")
ath.aa <- MSA2dist::cds2aa(ath)
aly.aa <- MSA2dist::cds2aa(aly)
## get CRBHit pairs
ath_aly_crbh <- aa2rbh(
    aa1=ath.aa,
    aa2=aly.aa,
    plotCurve=TRUE)
dim(ath_aly_crbh$crbh.pairs)
## get classical reciprocal best hit (RBHit) pairs
ath_aly_rbh <- aa2rbh(
    aa1=ath.aa,
    aa2=aly.aa,
    crbh=FALSE)
dim(ath_aly_rbh$crbh.pairs)
## selfblast
ath_selfblast_crbh <- aa2rbh(
    aa1=ath.aa,
    aa2=ath.aa,
    plotCurve=TRUE)
## see ?cds2rbh for more examples

---

aadir2orthofinder

Description

This function calculates (conditional-)reciprocal best hit (CRBHit) pairs for all possible comparison including self comparison from a directory of AA fasta files. Sequence searches are performed with last Kiełbasa, SM et al. (2011) [default] or with mmseqs2 Steinegger, M and Soeding, J (2017) or with diamond Buchfink, B et al. (2021).

Usage

aadir2orthofinder(
  dir,
  file_ending = "*",
  searchtool = "last",
  lastpath = file.path(find.package("CRBHits"), "extdata", "last-1639", "bin"),
  lastD = 1e+06,
  lastm = 10,
  mmseqs2path = NULL,
  mmseqs2sensitivity = 5.7,
  mmseqs2maxseqs = 300,
  diamondpath = NULL,
  diamondsensitivity = "--sensitive",
  diamondmaxtargetseqs = 0,
  lambda3path = NULL,
  lambda3sensitivity = "sensitive",
  lambda3nummatches = 25,
  outpath = "/tmp",
  crbh = TRUE,
  keepSingleDirection = FALSE,
  eval = 0.001,
  qcov = 0,
  tcov = 0,
  pident = 0,
  alnlen = 0,
  rost1999 = FALSE,
  filter = NULL,
  fit.type = "mean",
  fit.varweight = 0.1,
  fit.min = 5,
  threads = 1,
  remove = TRUE
)

Arguments

dir	directory containing AA fasta files [mandatory]
file_ending	define file ending to consider [default: *]
searchtool	specify sequence search algorithm last, mmseqs2, diamond or lambda3 [default: last]
lastpath	specify the PATH to the last binaries [default: /extdata/last-1639/bin/]
lastD	last option D: query letters per random alignment [default: 1e6]
lastm	last option m: maximum initial matches per query position [default: 10]
mmseqs2path	specify the PATH to the mmseqs2 binaries [default: NULL]
mmseqs2sensitivity	specify the sensitivity option of mmseqs2 [default: 5.7]
mmseqs2maxseqs	mmseqs2 option: Maximum results per query sequence allowed to pass the prefilter [default: 300]
diamondpath	specify the PATH to the diamond binaries [default: NULL]
diamondsensitivity	specify the sensitivity option of diamond [default: –sensitive]
diamondmaxtargetseqs	specify the maximum number of target sequences per query option of diamond [default: 0]
lambda3path	specify the PATH to the lambda3 binaries [default: NULL]
lambda3sensitivity	specify the sensitivity option of lambda3 [default: sensitive]
lambda3nummatches	specify the number of matches per query option of lambda3 [default: 25]
outpath	specify the output PATH [default: /tmp]
crbh	specify if conditional-reciprocal hit pairs should be retained as secondary hits [default: TRUE]
keepSingleDirection	specify if single direction secondary hit pairs should be retained [default: FALSE]
eval	evalue [default: 1e-3]
qcov	query coverage [default: 0.0]
tcov	target coverage [default: 0.0]
pident	percent identity [default: 0.0]
alnlen	alignment length [default: 0.0]
rost1999	specify if hit pairs should be filter by equation 2 of Rost 1999 [default: FALSE]
filter	specify additional custom filters as list to be applied on hit pairs [default: NULL]
fit.type	specify if mean or median should be used for fitting [default: mean]
fit.varweight	factor for fitting function to consider neighborhood [default: 0.1]
fit.min	specify minimum neighborhood alignment length [default: 5]
threads	number of parallel threads [default: 1]
remove	specify if last result files should be removed [default: TRUE]

Value

List of three (crbh=FALSE)

Author(s)

Kristian K Ullrich

References

Aubry S, Kelly S et al. (2014) Deep Evolutionary Comparison of Gene Expression Identifies Parallel Recruitment of Trans-Factors in Two Independent Origins of C4 Photosynthesis. PLOS Genetics, 10(6) e1004365.

Kiełbasa, SM et al. (2011) Adaptive seeds tame genomic sequence comparison. Genome research, 21(3), 487-493.

Rost B. (1999). Twilight zone of protein sequence alignments. Protein Engineering, 12(2), 85-94.

See Also

aafile2rbh

Examples

## compile last-1639 within CRBHits
CRBHits::make_last()

---

aafile2rbh

Description

This function calculates (conditional-)reciprocal best hit (CRBHit) pairs from two AA fasta files. Conditional-reciprocal best hit pairs were introduced by Aubry S, Kelly S et al. (2014). Sequence searches are performed with last Kiełbasa, SM et al. (2011) [default] or with mmseqs2 Steinegger, M and Soeding, J (2017) or with diamond Buchfink, B et al. (2021). If one specifies aafile1 and aafile2 as the same input a selfblast is conducted.

Usage

aafile2rbh(
  aafile1,
  aafile2,
  dbfile1 = NULL,
  dbfile2 = NULL,
  searchtool = "last",
  lastpath = file.path(find.package("CRBHits"), "extdata", "last-1639", "bin"),
  lastD = 1e+06,
  lastm = 10,
  mmseqs2path = NULL,
  mmseqs2sensitivity = 5.7,
  mmseqs2maxseqs = 300,
  diamondpath = NULL,
  diamondsensitivity = "--sensitive",
  diamondmaxtargetseqs = 0,
  lambda3path = NULL,
  lambda3sensitivity = "sensitive",
  lambda3nummatches = 25,
  outpath = "/tmp",
  crbh = TRUE,
  keepSingleDirection = FALSE,
  eval = 0.001,
  qcov = 0,
  tcov = 0,
  pident = 0,
  alnlen = 0,
  rost1999 = FALSE,
  filter = NULL,
  plotCurve = FALSE,
  fit.type = "mean",
  fit.varweight = 0.1,
  fit.min = 5,
  threads = 1,
  aafile2tmp = TRUE,
  remove = TRUE,
  remove.db = TRUE
)

Arguments

aafile1	aa1 fasta file [mandatory]
aafile2	aa2 fasta file [mandatory]
dbfile1	aa1 db file [optional]
dbfile2	aa2 db file [optional]
searchtool	specify sequence search algorithm last, mmseqs2, diamond or lambda3 [default: last]
lastpath	specify the PATH to the last binaries [default: /extdata/last-1639/bin/]
lastD	last option D: query letters per random alignment [default: 1e6]
lastm	last option m: maximum initial matches per query position [default: 10]
mmseqs2path	specify the PATH to the mmseqs2 binaries [default: NULL]
mmseqs2sensitivity	specify the sensitivity option of mmseqs2 [default: 5.7]
mmseqs2maxseqs	mmseqs2 option: Maximum results per query sequence allowed to pass the prefilter [default: 300]
diamondpath	specify the PATH to the diamond binaries [default: NULL]
diamondsensitivity	specify the sensitivity option of diamond [default: –sensitive]
diamondmaxtargetseqs	specify the maximum number of target sequences per query option of diamond [default: 0]
lambda3path	specify the PATH to the lambda3 binaries [default: NULL]
lambda3sensitivity	specify the sensitivity option of lambda3 [default: sensitive]
lambda3nummatches	specify the number of matches per query option of lambda3 [default: 25]
outpath	specify the output PATH [default: /tmp]
crbh	specify if conditional-reciprocal hit pairs should be retained as secondary hits [default: TRUE]
keepSingleDirection	specify if single direction secondary hit pairs should be retained [default: FALSE]
eval	evalue [default: 1e-3]
qcov	query coverage [default: 0.0]
tcov	target coverage [default: 0.0]
pident	percent identity [default: 0.0]
alnlen	alignment length [default: 0.0]
rost1999	specify if hit pairs should be filter by equation 2 of Rost 1999 [default: FALSE]
filter	specify additional custom filters as list to be applied on hit pairs [default: NULL]
plotCurve	specify if crbh fitting curve should be plotted [default: FALSE]
fit.type	specify if mean or median should be used for fitting [default: mean]
fit.varweight	factor for fitting function to consider neighborhood [default: 0.1]
fit.min	specify minimum neighborhood alignment length [default: 5]
threads	number of parallel threads [default: 1]
aafile2tmp	specify if aa input files sequenceIDs should be reduced to the first word and be written to a temporary aa file [default: TRUE]
remove	specify if last result files should be removed [default: TRUE]
remove.db	specify if last db files should be removed [default: TRUE]

Value

List of three (crbh=FALSE)
1: $crbh.pairs
2: $crbh1 matrix; query > target
3: $crbh2 matrix; target > query

List of four (crbh=TRUE)
1: $crbh.pairs
2: $crbh1 matrix; query > target
3: $crbh2 matrix; target > query
4: $rbh1_rbh2_fit; evalue fitting function

Author(s)

Kristian K Ullrich

References

Aubry S, Kelly S et al. (2014) Deep Evolutionary Comparison of Gene Expression Identifies Parallel Recruitment of Trans-Factors in Two Independent Origins of C4 Photosynthesis. PLOS Genetics, 10(6) e1004365.

Kiełbasa, SM et al. (2011) Adaptive seeds tame genomic sequence comparison. Genome research, 21(3), 487-493.

Rost B. (1999). Twilight zone of protein sequence alignments. Protein Engineering, 12(2), 85-94.

See Also

aa2rbh

Examples

## compile last-1639 within CRBHits
CRBHits::make_last()
## load example sequence data
athfile <- system.file("fasta", "ath.aa.fasta.gz", package="CRBHits")
alyfile <- system.file("fasta", "aly.aa.fasta.gz", package="CRBHits")
## get CRBHit pairs
ath_aly_crbh <- aafile2rbh(
    aafile1=athfile,
    aafile2=alyfile,
    plotCurve=TRUE)
dim(ath_aly_crbh$crbh.pairs)
## get classical reciprocal best hit (RBHit) pairs
ath_aly_rbh <- aafile2rbh(
    aafile1=athfile,
    aafile2=alyfile,
    crbh=FALSE)
dim(ath_aly_rbh$crbh.pairs)
## selfblast
ath_selfblast_crbh <- aafile2rbh(
    aafile1=athfile,
    aafile2=athfile,
    plotCurve=TRUE)
## see ?cds2rbh for more examples

---

aafile2rbhplus

Description

This function calculates (conditional-)reciprocal best hit (CRBHit) pairs from two AA fasta files. Conditional-reciprocal best hit pairs were introduced by Aubry S, Kelly S et al. (2014). Sequence searches are performed with last Kiełbasa, SM et al. (2011) [default] or with mmseqs2 Steinegger, M and Soeding, J (2017) or with diamond Buchfink, B et al. (2021). If one specifies aafile1 and aafile2 as the same input a selfblast is conducted.

Usage

aafile2rbhplus(
  aafile1,
  aafile2,
  dbfile1 = NULL,
  dbfile2 = NULL,
  searchtool = "last",
  lastpath = file.path(find.package("CRBHits"), "extdata", "last-1639", "bin"),
  lastD = 1e+06,
  lastm = 10,
  mafconvertpath = paste0(find.package("CRBHits"), "/extdata/maf-convert-crbhits"),
  mmseqs2path = NULL,
  mmseqs2sensitivity = 5.7,
  mmseqs2maxseqs = 300,
  diamondpath = NULL,
  diamondsensitivity = "--sensitive",
  diamondmaxtargetseqs = 0,
  lambda3path = NULL,
  lambda3sensitivity = "sensitive",
  lambda3nummatches = 25,
  outpath = "/tmp",
  crbh = TRUE,
  keepSingleDirection = FALSE,
  eval = 0.001,
  qcov = 0,
  tcov = 0,
  pident = 0,
  alnlen = 0,
  rost1999 = FALSE,
  filter = NULL,
  plotCurve = FALSE,
  fit.type = "mean",
  fit.varweight = 0.1,
  fit.min = 5,
  threads = 1,
  aafile2tmp = TRUE,
  remove = TRUE,
  remove.db = TRUE
)

Arguments

aafile1	aa1 fasta file [mandatory]
aafile2	aa2 fasta file [mandatory]
dbfile1	aa1 db file [optional]
dbfile2	aa2 db file [optional]
searchtool	specify sequence search algorithm last, mmseqs2, diamond or lambda3 [default: last]
lastpath	specify the PATH to the last binaries [default: /extdata/last-1639/bin/]
lastD	last option D: query letters per random alignment [default: 1e6]
lastm	last option m: maximum initial matches per query position [default: 10]
mafconvertpath	specify the PATH to the maf-convert script [default: /extdata/maf-convert-crbhits]
mmseqs2path	specify the PATH to the mmseqs2 binaries [default: NULL]
mmseqs2sensitivity	specify the sensitivity option of mmseqs2 [default: 5.7]
mmseqs2maxseqs	mmseqs2 option: Maximum results per query sequence allowed to pass the prefilter [default: 300]
diamondpath	specify the PATH to the diamond binaries [default: NULL]
diamondsensitivity	specify the sensitivity option of diamond [default: –sensitive]
diamondmaxtargetseqs	specify the maximum number of target sequences per query option of diamond [default: 0]
lambda3path	specify the PATH to the lambda3 binaries [default: NULL]
lambda3sensitivity	specify the sensitivity option of lambda3 [default: sensitive]
lambda3nummatches	specify the number of matches per query option of lambda3 [default: 25]
outpath	specify the output PATH [default: /tmp]
crbh	specify if conditional-reciprocal hit pairs should be retained as secondary hits [default: TRUE]
keepSingleDirection	specify if single direction secondary hit pairs should be retained [default: FALSE]
eval	evalue [default: 1e-3]
qcov	query coverage [default: 0.0]
tcov	target coverage [default: 0.0]
pident	percent identity [default: 0.0]
alnlen	alignment length [default: 0.0]
rost1999	specify if hit pairs should be filter by equation 2 of Rost 1999 [default: FALSE]
filter	specify additional custom filters as list to be applied on hit pairs [default: NULL]
plotCurve	specify if crbh fitting curve should be plotted [default: FALSE]
fit.type	specify if mean or median should be used for fitting [default: mean]
fit.varweight	factor for fitting function to consider neighborhood [default: 0.1]
fit.min	specify minimum neighborhood alignment length [default: 5]
threads	number of parallel threads [default: 1]
aafile2tmp	specify if aa input files sequenceIDs should be reduced to the first word and be written to a temporary aa file [default: TRUE]
remove	specify if last result files should be removed [default: TRUE]
remove.db	specify if last db files should be removed [default: TRUE]

Value

List of three (crbh=FALSE)
1: $crbh.pairs
2: $crbh1 matrix; query > target
3: $crbh2 matrix; target > query

List of four (crbh=TRUE)
1: $crbh.pairs
2: $crbh1 matrix; query > target
3: $crbh2 matrix; target > query
4: $rbh1_rbh2_fit; evalue fitting function

Author(s)

Kristian K Ullrich

References

Aubry S, Kelly S et al. (2014) Deep Evolutionary Comparison of Gene Expression Identifies Parallel Recruitment of Trans-Factors in Two Independent Origins of C4 Photosynthesis. PLOS Genetics, 10(6) e1004365.

Kiełbasa, SM et al. (2011) Adaptive seeds tame genomic sequence comparison. Genome research, 21(3), 487-493.

Rost B. (1999). Twilight zone of protein sequence alignments. Protein Engineering, 12(2), 85-94.

See Also

aa2rbh

Examples

## compile last-1639 within CRBHits
CRBHits::make_last()
## load example sequence data
athfile <- system.file("fasta", "ath.aa.fasta.gz", package="CRBHits")
alyfile <- system.file("fasta", "aly.aa.fasta.gz", package="CRBHits")
## get CRBHit pairs
ath_aly_crbh <- aafile2rbhplus(
    aafile1=athfile,
    aafile2=alyfile,
    plotCurve=TRUE)
dim(ath_aly_crbh$crbh.pairs)
## get classical reciprocal best hit (RBHit) pairs
ath_aly_rbh <- aafile2rbhplus(
    aafile1=athfile,
    aafile2=alyfile,
    crbh=FALSE)
dim(ath_aly_rbh$crbh.pairs)
## selfblast
ath_selfblast_crbh <- aafile2rbhplus(
    aafile1=athfile,
    aafile2=athfile,
    plotCurve=TRUE)
## see ?cds2rbh for more examples

---

aly-data

Description

Example cds sequences from Arabidopsis lyrata as DNAStringSet.

Usage

data(aly)

Format

an object of class DNAStringSet see XStringSet-class

Examples

data("aly", package="CRBHits")

---

ath_aly_crbh-data

Description

Example conditional-reciprocal best hit (CRBHit) pair results.

Usage

data(ath_aly_crbh)

Format

an object of class list

Examples

data("ath_aly_crbh", package="CRBHits")

---

ath_aly_ncbi_dagchainer-data

Description

Example of DAGchainer results between Arabidopsis thalina and Arabidopsis lyrata obtained from NCBI.

Usage

data(ath_aly_ncbi_dagchainer)

Format

an object of class list

Examples

data("ath_aly_ncbi_dagchainer", package="CRBHits")

---

ath_aly_ncbi_kaks-data

Description

Example of Ka/Ks values between Arabidopsis thalina and Arabidopsis lyrata obtained from NCBI.

Usage

data(ath_aly_ncbi_kaks)

Format

an object of class list

Examples

data("ath_aly_ncbi_kaks", package="CRBHits")

---

ath-data

Description

Example cds sequences from Arabidopsis thaliana as DNAStringSet.

Usage

data(ath)

Format

an object of class DNAStringSet see XStringSet-class

Examples

data("ath", package="CRBHits")

---

cds2genepos

Description

This function extracts the gene position from either NCBI or ENSEMBL CDS input.

Usage

cds2genepos(cds, source = "NCBI", keep.names = NULL)

Arguments

cds	DNAStringSet [mandatory]
source	source indicating either NCBI or ENSEMBL [default: NCBI]
keep.names	vector indicating gene ids to be kept before chromosomal position assignment [default: NULL]

Value

matrix 1: $gene.seq.id
2: $gene.chr
3: $gene.start
4: $gene.end
5: $gene.mid
6: $gene.strand
7: $gene.idx

Author(s)

Kristian K Ullrich

See Also

isoform2longest

Examples

## load example sequence data
data("ath", package="CRBHits")
ath.genepos <- cds2genepos(
    cds=ath,
    source="ENSEMBL")
## Not run: 
## load example sequence data
## set EnsemblPlants URL
ensemblPlants <- "ftp://ftp.ensemblgenomes.org/pub/plants/release-48/fasta/"
## set Arabidopsis thaliana CDS URL
ARATHA.cds.url <- paste0(ensemblPlants,
    "arabidopsis_thaliana/cds/Arabidopsis_thaliana.TAIR10.cds.all.fa.gz")
ARATHA.cds.file <- tempfile()
## download CDS
download.file(ARATHA.cds.url, ARATHA.cds.file, quiet=FALSE)
ARATHA.cds <- Biostrings::readDNAStringSet(ARATHA.cds.file)
## get gene position
ARATHA.cds.genepos <- cds2genepos(ARATHA.cds, "ENSEMBL")

## End(Not run)

---

cds2rbh

Description

This function calculates (conditional-)reciprocal best hit (CRBHit) pairs from two CDS DNAStringSet's. CRBHit pairs were introduced by Aubry S, Kelly S et al. (2014). Sequence searches are performed with last Kiełbasa, SM et al. (2011) [default] or with mmseqs2 Steinegger, M and Soeding, J (2017) or with diamond Buchfink, B et al. (2021). If one specifies cds1 and cds2 as the same input a selfblast is conducted.

Usage

cds2rbh(
  cds1,
  cds2,
  dbfile1 = NULL,
  dbfile2 = NULL,
  searchtool = "last",
  lastpath = file.path(find.package("CRBHits"), "extdata", "last-1639", "bin"),
  lastD = 1e+06,
  lastm = 10,
  mmseqs2path = NULL,
  mmseqs2sensitivity = 5.7,
  mmseqs2maxseqs = 300,
  diamondpath = NULL,
  diamondsensitivity = "--sensitive",
  diamondmaxtargetseqs = 0,
  lambda3path = NULL,
  lambda3sensitivity = "sensitive",
  lambda3nummatches = 25,
  outpath = "/tmp",
  crbh = TRUE,
  keepSingleDirection = FALSE,
  eval = 0.001,
  qcov = 0,
  tcov = 0,
  pident = 0,
  alnlen = 0,
  rost1999 = FALSE,
  filter = NULL,
  plotCurve = FALSE,
  fit.type = "mean",
  fit.varweight = 0.1,
  fit.min = 5,
  longest.isoform = FALSE,
  isoform.source = "NCBI",
  threads = 1,
  remove = TRUE,
  remove.db = TRUE,
  shorten1 = FALSE,
  frame1 = 1,
  framelist1 = NULL,
  genetic.code1 = NULL,
  shorten2 = FALSE,
  frame2 = 1,
  framelist2 = NULL,
  genetic.code2 = NULL
)

Arguments

cds1	cds1 sequences as DNAStringSet [mandatory]
cds2	cds2 sequences as DNAStringSet [mandatory]
dbfile1	aa1 db file [optional]
dbfile2	aa2 db file [optional]
searchtool	specify sequence search algorithm last, mmseqs2, diamond or lambda3 [default: last]
lastpath	specify the PATH to the last binaries [default: /extdata/last-1639/bin/]
lastD	last option D: query letters per random alignment [default: 1e6]
lastm	last option m: maximum initial matches per query position [default: 10]
mmseqs2path	specify the PATH to the mmseqs2 binaries [default: NULL]
mmseqs2sensitivity	specify the sensitivity option of mmseqs2 [default: 5.7]
mmseqs2maxseqs	mmseqs2 option: Maximum results per query sequence allowed to pass the prefilter [default: 300]
diamondpath	specify the PATH to the diamond binaries [default: NULL]
diamondsensitivity	specify the sensitivity option of diamond [default: –sensitive]
diamondmaxtargetseqs	specify the maximum number of target sequences per query option of diamond [default: 0]
lambda3path	specify the PATH to the lambda3 binaries [default: NULL]
lambda3sensitivity	specify the sensitivity option of lambda3 [default: sensitive]
lambda3nummatches	specify the number of matches per query option of lambda3 [default: 25]
outpath	specify the output PATH [default: /tmp]
crbh	specify if conditional-reciprocal hit pairs should be retained as secondary hits [default: TRUE]
keepSingleDirection	specify if single direction secondary hit pairs should be retained [default: FALSE]
eval	evalue [default: 1e-3]
qcov	query coverage [default: 0.0]
tcov	target coverage [default: 0.0]
pident	percent identity [default: 0.0]
alnlen	alignment length [default: 0.0]
rost1999	specify if hit pairs should be filter by equation 2 of Rost 1999 [default: FALSE]
filter	specify additional custom filters as list to be applied on hit pairs [default: NULL]
plotCurve	specify if crbh fitting curve should be plotted [default: FALSE]
fit.type	specify if mean or median should be used for fitting [default: mean]
fit.varweight	factor for fitting function to consider neighborhood [default: 0.1]
fit.min	specify minimum neighborhood alignment length [default: 5]
longest.isoform	specify if cds sequences should be reduced to the longest isoform (only possible if data was accessed from NCBI or ENSEMBL) [default: FALSE]
isoform.source	specify cds sequences source (either NCBI or ENSEMBL) [default: NCBI]
threads	number of parallel threads [default: 1]
remove	specify if last result files should be removed [default: TRUE]
remove.db	specify if last db files should be removed [default: TRUE]
shorten1	shorten all sequences to multiple of three [default: FALSE]
frame1	indicates the first base of the first codon [default: 1]
framelist1	supply vector of frames for each entry [default: NULL]
genetic.code1	The genetic code to use for the translation of codons into Amino Acid letters [default: NULL]
shorten2	shorten all sequences to multiple of three [default: FALSE]
frame2	indicates the first base of the first codon [default: 1]
framelist2	supply vector of frames for each entry [default: NULL]
genetic.code2	The genetic code to use for the translation of codons into Amino Acid letters [default: NULL]

Value

List of three (crbh=FALSE)
1: $crbh.pairs
2: $crbh1 matrix; query > target
3: $crbh2 matrix; target > query

List of four (crbh=TRUE)
1: $crbh.pairs
2: $crbh1 matrix; query > target
3: $crbh2 matrix; target > query
4: $rbh1_rbh2_fit; evalue fitting function

Author(s)

Kristian K Ullrich

References

Aubry S, Kelly S et al. (2014) Deep Evolutionary Comparison of Gene Expression Identifies Parallel Recruitment of Trans-Factors in Two Independent Origins of C4 Photosynthesis. PLOS Genetics, 10(6) e1004365.

Kiełbasa, SM et al. (2011) Adaptive seeds tame genomic sequence comparison. Genome research, 21(3), 487-493.

Rost B. (1999). Twilight zone of protein sequence alignments. Protein Engineering, 12(2), 85-94.

See Also

cdsfile2rbh, isoform2longest

Examples

## compile last-1639 within CRBHits
CRBHits::make_last()
## load example sequence data
data("ath", package="CRBHits")
data("aly", package="CRBHits")
## get CRBHit pairs
ath_aly_crbh <- cds2rbh(
    cds1=ath,
    cds2=aly,
    plotCurve=TRUE)
dim(ath_aly_crbh$crbh.pairs)
## get classical reciprocal best hit (RBHit) pairs
ath_aly_rbh <- cds2rbh(
    cds1=ath,
    cds2=aly,
    crbh=FALSE)
dim(ath_aly_rbh$crbh.pairs)
## filter for evalue 1e-100
ath_aly_crbh.eval100 <- cds2rbh(
    cds1=ath,
    cds2=aly,
    eval=1e-100)
dim(ath_aly_crbh.eval100$crbh.pairs)
## filter for query coverage
ath_aly_crbh.qcov <- cds2rbh(
    cds1=ath,
    cds2=aly,
    qcov=0.5)
dim(ath_aly_crbh.qcov$crbh.pairs)
## custom filter for e.g. bit score (column 12)
## Note: multiple filters can be given in filter param as list
myfilter <- function(rbh, value=500.0){
    return(rbh[as.numeric(rbh[, 12])>=value, , drop=FALSE])
}
ath_aly_crbh.custom <- cds2rbh(
    cds1=ath,
    cds2=aly,
    filter=list(myfilter))
dim(ath_aly_crbh.custom$crbh.pairs)
## selfblast
ath_selfblast_crbh <- cds2rbh(
    cds1=ath,
    cds2=ath,
    plotCurve=TRUE)

---

cdsdir2orthofinder

Description

This function calculates (conditional-)reciprocal best hit (CRBHit) pairs for all possible comparison including self comparison from a directory of CDS fasta files. Sequence searches are performed with last Kiełbasa, SM et al. (2011) [default] or with mmseqs2 Steinegger, M and Soeding, J (2017) or with diamond Buchfink, B et al. (2021).

Usage

cdsdir2orthofinder(
  dir,
  file_ending = "*",
  searchtool = "last",
  lastpath = file.path(find.package("CRBHits"), "extdata", "last-1639", "bin"),
  lastD = 1e+06,
  lastm = 10,
  mmseqs2path = NULL,
  mmseqs2sensitivity = 5.7,
  mmseqs2maxseqs = 300,
  diamondpath = NULL,
  diamondsensitivity = "--sensitive",
  diamondmaxtargetseqs = 0,
  lambda3path = NULL,
  lambda3sensitivity = "sensitive",
  lambda3nummatches = 25,
  outpath = "/tmp",
  dbpath = "/tmp",
  crbh = TRUE,
  keepSingleDirection = FALSE,
  eval = 0.001,
  qcov = 0,
  tcov = 0,
  pident = 0,
  alnlen = 0,
  rost1999 = FALSE,
  filter = NULL,
  fit.type = "mean",
  fit.varweight = 0.1,
  fit.min = 5,
  threads = 1,
  remove = FALSE,
  remove.db = FALSE
)

Arguments

dir	directory containing CDS fasta files [mandatory]
file_ending	define file ending to consider [default: *]
searchtool	specify sequence search algorithm last, mmseqs2, diamond or lambda3 [default: last]
lastpath	specify the PATH to the last binaries [default: /extdata/last-1639/bin/]
lastD	last option D: query letters per random alignment [default: 1e6]
lastm	last option m: maximum initial matches per query position [default: 10]
mmseqs2path	specify the PATH to the mmseqs2 binaries [default: NULL]
mmseqs2sensitivity	specify the sensitivity option of mmseqs2 [default: 5.7]
mmseqs2maxseqs	mmseqs2 option: Maximum results per query sequence allowed to pass the prefilter [default: 300]
diamondpath	specify the PATH to the diamond binaries [default: NULL]
diamondsensitivity	specify the sensitivity option of diamond [default: –sensitive]
diamondmaxtargetseqs	specify the maximum number of target sequences per query option of diamond [default: 0]
lambda3path	specify the PATH to the lambda3 binaries [default: NULL]
lambda3sensitivity	specify the sensitivity option of lambda3 [default: sensitive]
lambda3nummatches	specify the number of matches per query option of lambda3 [default: 25]
outpath	specify the output PATH [default: /tmp]
dbpath	specify the output PATH [default: /tmp]
crbh	specify if conditional-reciprocal hit pairs should be retained as secondary hits [default: TRUE]
keepSingleDirection	specify if single direction secondary hit pairs should be retained [default: FALSE]
eval	evalue [default: 1e-3]
qcov	query coverage [default: 0.0]
tcov	target coverage [default: 0.0]
pident	percent identity [default: 0.0]
alnlen	alignment length [default: 0.0]
rost1999	specify if hit pairs should be filter by equation 2 of Rost 1999 [default: FALSE]
filter	specify additional custom filters as list to be applied on hit pairs [default: NULL]
fit.type	specify if mean or median should be used for fitting [default: mean]
fit.varweight	factor for fitting function to consider neighborhood [default: 0.1]
fit.min	specify minimum neighborhood alignment length [default: 5]
threads	number of parallel threads [default: 1]
remove	specify if last result files should be removed [default: TRUE]
remove.db	specify if last db files should be removed [default: TRUE]

Value

List of three (crbh=FALSE)

Author(s)

Kristian K Ullrich

References

Aubry S, Kelly S et al. (2014) Deep Evolutionary Comparison of Gene Expression Identifies Parallel Recruitment of Trans-Factors in Two Independent Origins of C4 Photosynthesis. PLOS Genetics, 10(6) e1004365.

Kiełbasa, SM et al. (2011) Adaptive seeds tame genomic sequence comparison. Genome research, 21(3), 487-493.

Rost B. (1999). Twilight zone of protein sequence alignments. Protein Engineering, 12(2), 85-94.

See Also

aafile2rbh

Examples

## compile last-1639 within CRBHits
CRBHits::make_last()

---

cdsfile2aafile

Description

This function translates a cds fasta file into an aa fasta file.

Usage

cdsfile2aafile(
  infile,
  outfile,
  shorten = FALSE,
  frame = 1,
  framelist = NULL,
  genetic.code = NULL
)

Arguments

infile	cds fasta file [mandatory]
outfile	aa fasta file [mandatory]
shorten	shorten all sequences to multiple of three [default: FALSE]
frame	indicates the first base of a the first codon [default: 1]
framelist	supply vector of frames for each entry [default: NULL]
genetic.code	The genetic code to use for the translation of codons into Amino Acid letters [default: NULL]

Value

aa fasta file

Author(s)

Kristian K Ullrich

See Also

cds2aa

Examples

## define file path
cdsfile <- system.file("fasta", "ath.cds.fasta.gz", package="CRBHits")
## create empty temp file
aafile <- tempfile()
## convert input CDS fasta file into AA fasta file
cdsfile2aafile(cdsfile, aafile)
aa <- Biostrings::readAAStringSet(aafile)
aa

---

cdsfile2rbh

Description

This function calculates (conditional-)reciprocal best hit (CRBHit) pairs from two CDS fasta files. CRBHit pairs were introduced by Aubry S, Kelly S et al. (2014). Sequence searches are performed with last Kiełbasa, SM et al. (2011) [default] or with mmseqs2 Steinegger, M and Soeding, J (2017) or with diamond Buchfink, B et al. (2021). If one specifies cdsfile1 and cdsfile2 as the same input a selfblast is conducted.

Usage

cdsfile2rbh(
  cdsfile1,
  cdsfile2,
  dbfile1 = NULL,
  dbfile2 = NULL,
  searchtool = "last",
  lastpath = file.path(find.package("CRBHits"), "extdata", "last-1639", "bin"),
  lastD = 1e+06,
  lastm = 10,
  mmseqs2path = NULL,
  mmseqs2sensitivity = 5.7,
  mmseqs2maxseqs = 300,
  diamondpath = NULL,
  diamondsensitivity = "--sensitive",
  diamondmaxtargetseqs = 0,
  lambda3path = NULL,
  lambda3sensitivity = "sensitive",
  lambda3nummatches = 25,
  outpath = "/tmp",
  crbh = TRUE,
  keepSingleDirection = FALSE,
  eval = 0.001,
  qcov = 0,
  tcov = 0,
  pident = 0,
  alnlen = 0,
  rost1999 = FALSE,
  filter = NULL,
  plotCurve = FALSE,
  fit.type = "mean",
  fit.varweight = 0.1,
  fit.min = 5,
  longest.isoform = FALSE,
  isoform.source = "NCBI",
  threads = 1,
  remove = TRUE,
  remove.db = TRUE,
  shorten1 = FALSE,
  frame1 = 1,
  framelist1 = NULL,
  genetic.code1 = NULL,
  shorten2 = FALSE,
  frame2 = 1,
  framelist2 = NULL,
  genetic.code2 = NULL
)

Arguments

cdsfile1	cds1 fasta file [mandatory]
cdsfile2	cds2 fasta file [mandatory]
dbfile1	aa1 db file [optional]
dbfile2	aa2 db file [optional]
searchtool	specify sequence search algorithm last, mmseqs2, diamond or lambda3 [default: last]
lastpath	specify the PATH to the last binaries [default: /extdata/last-1639/bin/]
lastD	last option D: query letters per random alignment [default: 1e6]
lastm	last option m: maximum initial matches per query position [default: 10]
mmseqs2path	specify the PATH to the mmseqs2 binaries [default: NULL]
mmseqs2sensitivity	specify the sensitivity option of mmseqs2 [default: 5.7]
mmseqs2maxseqs	mmseqs2 option: Maximum results per query sequence allowed to pass the prefilter [default: 300]
diamondpath	specify the PATH to the diamond binaries [default: NULL]
diamondsensitivity	specify the sensitivity option of diamond [default: –sensitive]
diamondmaxtargetseqs	specify the maximum number of target sequences per query option of diamond [default: 0]
lambda3path	specify the PATH to the lambda3 binaries [default: NULL]
lambda3sensitivity	specify the sensitivity option of lambda3 [default: sensitive]
lambda3nummatches	specify the number of matches per query option of lambda3 [default: 25]
outpath	specify the output PATH [default: /tmp]
crbh	specify if conditional-reciprocal hit pairs should be retained as secondary hits [default: TRUE]
keepSingleDirection	specify if single direction secondary hit pairs should be retained [default: FALSE]
eval	evalue [default: 1e-3]
qcov	query coverage [default: 0.0]
tcov	target coverage [default: 0.0]
pident	percent identity [default: 0.0]
alnlen	alignment length [default: 0.0]
rost1999	specify if hit pairs should be filter by equation 2 of Rost 1999 [default: FALSE]
filter	specify additional custom filters as list to be applied on hit pairs [default: NULL]
plotCurve	specify if crbh fitting curve should be plotted [default: FALSE]
fit.type	specify if mean or median should be used for fitting [default: mean]
fit.varweight	factor for fitting function to consider neighborhood [default: 0.1]
fit.min	specify minimum neighborhood alignment length [default: 5]
longest.isoform	specify if cds sequences should be removed to the longest isoform (only possible if data was accessed from NCBI or ENSEMBL) [default: FALSE]
isoform.source	specify cds sequences source (either NCBI or ENSEMBL) [default: NCBI]
threads	number of parallel threads [default: 1]
remove	specify if last result files should be removed [default: TRUE]
remove.db	specify if last db files should be removed [default: TRUE]
shorten1	shorten all sequences to multiple of three [default: FALSE]
frame1	indicates the first base of the first codon [default: 1]
framelist1	supply vector of frames for each entry [default: NULL]
genetic.code1	The genetic code to use for the translation of codons into Amino Acid letters [default: NULL]
shorten2	shorten all sequences to multiple of three [default: FALSE]
frame2	indicates the first base of the first codon [default: 1]
framelist2	supply vector of frames for each entry [default: NULL]
genetic.code2	The genetic code to use for the translation of codons into Amino Acid letters [default: NULL]

Value

List of three (crbh=FALSE)
1: $crbh.pairs
2: $crbh1 matrix; query > target
3: $crbh2 matrix; target > query

List of four (crbh=TRUE)
1: $crbh.pairs
2: $crbh1 matrix; query > target
3: $crbh2 matrix; target > query
4: $rbh1_rbh2_fit; evalue fitting function

Author(s)

Kristian K Ullrich

References

Aubry S, Kelly S et al. (2014) Deep Evolutionary Comparison of Gene Expression Identifies Parallel Recruitment of Trans-Factors in Two Independent Origins of C4 Photosynthesis. PLOS Genetics, 10(6) e1004365.

Kiełbasa, SM et al. (2011) Adaptive seeds tame genomic sequence comparison. Genome research, 21(3), 487-493.

Steinegger, M and Soeding, J. (2017). MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nature Biotechnology, 35, 1026-1028.

Rost B. (1999). Twilight zone of protein sequence alignments. Protein Engineering, 12(2), 85-94.

See Also

cds2rbh, isoform2longest

Examples

## compile last-1639 within CRBHits
CRBHits::make_last()
## load example sequence data
athfile <- system.file("fasta", "ath.cds.fasta.gz", package="CRBHits")
alyfile <- system.file("fasta", "aly.cds.fasta.gz", package="CRBHits")
## get CRBHit pairs
ath_aly_crbh <- cdsfile2rbh(
    cdsfile1=athfile,
    cdsfile2=alyfile,
    plotCurve=TRUE)
dim(ath_aly_crbh$crbh.pairs)
## get classical reciprocal best hit (RBHit) pairs
ath_aly_rbh <- cdsfile2rbh(
    cdsfile1=athfile,
    cdsfile2=alyfile,
    crbh=FALSE)
dim(ath_aly_rbh$crbh.pairs)
## selfblast
ath_selfblast_crbh <- cdsfile2rbh(
    cdsfile1=athfile,
    cdsfile2=athfile,
    plotCurve=TRUE)
## see ?cds2rbh for more examples

---

check_ext_install

Description

This function checks if external binary exists

Usage

check_ext_install(ext_name, ext_dir, binary_name = ext_name)

Arguments

ext_name	external tool name [mandatory]
ext_dir	external tool directory [mandatory]
binary_name	external binary name (per default ext_name) [mandatory]

Value

path of prerequisites

Author(s)

Kristian K Ullrich

---

col2transparent

Description

R color to transparent conversion.

Usage

col2transparent(col, alpha.perc = 0)

Arguments

col	R color name or R color pal [mandatory]
alpha.perc	an alpha-transparency level in percent [default: 0]

Value

A character vector with elements of 9 characters, "#" followed by the red, blue, green and alpha values in hexadecimal (after rescaling to 0 ... 255).

Author(s)

Kristian K Ullrich

See Also

palette

Examples

col2transparent("green", 50)
## Demonstrate the colors 1:8 in different palettes using a custom matplot()
sinplot <- function(main=NULL) {
    x <- outer(
        seq(-pi, pi, length.out = 50),
        seq(0, pi, length.out = 9),
        function(x, y) sin(x - y)
    )
    matplot(x, type = "l", lwd = 4, lty = 1, col = 1:9, ylab = "", main=main)
}
my.palette <- c(
    "#CBC106", "#27993C", "#1C6838",
    "#8EBCB5", "#389CA7", "#4D83AB",
    "#CB7B26", "#BF565D", "#9E163C")
palette(my.palette); sinplot("my.palette")
## 25% transparent
palette(col2transparent(palette(my.palette), 25));
    sinplot("my.palette - transparent")
## 50% transparent
palette(col2transparent(palette(my.palette), 50));
    sinplot("my.palette - transparent")
## 75% transparent
palette(col2transparent(palette(my.palette), 75));
    sinplot("my.palette - transparent")

---

CRBHitsColors

Description

CRBHits specific color palette.

Usage

CRBHitsColors(n, alpha.perc = 0)

Arguments

n	The number of colors (greater than or equal to 1) to be in the palette [mandatory]
alpha.perc	an alpha-transparency level in percent [default: 0]

Value

CRBHits specific color palette

Author(s)

Kristian K Ullrich

See Also

palette

Examples

plot(1:9, pch=20, col=CRBHitsColors(9), cex=3)
## use alpha
plot(1:9, pch=20, col=CRBHitsColors(9, 50), cex=3)

---

filter_alnlen

Description

This function filters BLAST-like tabular output according to alignment length.

Usage

filter_alnlen(rbh, alnlen = 0, inverse = FALSE)

Arguments

rbh	BLAST-like tabular matrix [mandatory]
alnlen	alignment length [default: 0.0]
inverse	specify if filter should keep the removed values [default: FALSE]

Value

rbh matrix

Author(s)

Kristian K Ullrich

Examples

## load crbh data
data(ath_aly_crbh)
dim(ath_aly_crbh$crbh1)
dim(filter_alnlen(
    rbh=ath_aly_crbh$crbh1,
    alnlen=75))

---

filter_eval

Description

This function filters BLAST-like tabular output according to evalue.

Usage

filter_eval(rbh, eval = 0.001, inverse = FALSE)

Arguments

rbh	BLAST-like tabular matrix [mandatory]
eval	evalue [default: 1e-3]
inverse	specify if filter should keep the removed values [default: FALSE]

Value

rbh matrix

Author(s)

Kristian K Ullrich

Examples

## load crbh data
data(ath_aly_crbh)
dim(ath_aly_crbh$crbh1)
dim(filter_eval(
    rbh=ath_aly_crbh$crbh1,
    eval=1e-100))

---

filter_pident

Description

This function filters BLAST-like tabular output according to protein identity.

Usage

filter_pident(rbh, pident = 0, inverse = FALSE)

Arguments

rbh	BLAST-like tabular matrix [mandatory]
pident	percent identity [default: 0.0]
inverse	specify if filter should keep the removed values [default: FALSE]

Value

rbh matrix

Author(s)

Kristian K Ullrich

Examples

## load crbh data
data(ath_aly_crbh)
dim(ath_aly_crbh$crbh1)
dim(filter_pident(
    rbh=ath_aly_crbh$crbh1,
    pident=75))

---

filter_qcov

Description

This function filters BLAST-like tabular output according to percentage query coverage.

Usage

filter_qcov(rbh, qcov = 0, inverse = FALSE)

Arguments

rbh	BLAST-like tabular matrix [mandatory]
qcov	query coverage [default: 0.0]
inverse	specify if filter should keep the removed values [default: FALSE]

Value

rbh matrix

Author(s)

Kristian K Ullrich

Examples

## load crbh data
data(ath_aly_crbh)
dim(ath_aly_crbh$crbh1)
dim(filter_qcov(
    rbh=ath_aly_crbh$crbh1,
    qcov=0.75))

---

filter_rost1999

Description

This function filters BLAST-like tabular output according to equation 2 of Rost 1999.

Usage

filter_rost1999(rbh, inverse = FALSE)

Arguments

rbh	BLAST-like tabular matrix [mandatory]
inverse	specify if filter should keep the removed values [default: FALSE]

Value

rbh matrix

Author(s)

Kristian K Ullrich

References

Rost B. (1999). Twilight zone of protein sequence alignments. Protein Engineering, 12(2), 85-94.

Examples

## load crbh data
data(ath_aly_crbh)
dim(ath_aly_crbh$crbh1)
dim(filter_rost1999(
    rbh=ath_aly_crbh$crbh1))

---

filter_tcov

Description

This function filters BLAST-like tabular output according to percentage target coverage.

Usage

filter_tcov(rbh, tcov = 0, inverse = FALSE)

Arguments

rbh	BLAST-like tabular matrix [mandatory]
tcov	target coverage [default: 0.0]
inverse	specify if filter should keep the removed values [default: FALSE]

Value

rbh matrix

Author(s)

Kristian K Ullrich

Examples

## load crbh data
data(ath_aly_crbh)
dim(ath_aly_crbh$crbh1)
dim(filter_tcov(
    rbh=ath_aly_crbh$crbh1,
    tcov=0.75))

---

gff2longest

Description

This function extracts the gene position from GFF3 input and optional extracts the longest isoform.

Usage

gff2longest(gff3file, cds = NULL, removeNonCoding = TRUE, source = "NCBI")

Arguments

gff3file	GFF3 path [mandatory]
cds	DNAStringSet [optional]
removeNonCoding	specify if NonCoding transcripts should be removed
source	source indicating either NCBI or ENSEMBL [default: NCBI]

Value

list

Author(s)

Kristian K Ullrich

See Also

XStringSet-class

Examples

## Not run: 
## load example sequence data
## set NCBI GFF3 URL
NCBI <- "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/"
ARATHA.NCBI.gff3.url <- paste0(NCBI,
    "GCF/000/001/735/GCF_000001735.4_TAIR10.1/",
    "GCF_000001735.4_TAIR10.1_genomic.gff.gz")
ARATHA.NCBI.gff3.file <- tempfile()
## download GTF file
download.file(ARATHA.NCBI.gff3.url, ARATHA.NCBI.gff3.file, quiet=FALSE)
## set NCBI CDS URL
ARATHA.NCBI.cds.url <- paste0(NCBI,
    "GCF/000/001/735/GCF_000001735.4_TAIR10.1/",
    "GCF_000001735.4_TAIR10.1_cds_from_genomic.fna.gz")
ARATHA.NCBI.cds.file <- tempfile()
## download CDS file
download.file(ARATHA.NCBI.cds.url, ARATHA.NCBI.cds.file, quiet=FALSE)
## load CDS
ARATHA.NCBI.cds <- Biostrings::readDNAStringSet(ARATHA.NCBI.cds.file)
## get genepos and longest isoform
ARATHA.NCBI.gff3.longest <- gff2longest(gtffile=ARATHA.NCBI.gff3.file,
    cds=ARATHA.NCBI.cds, source="NCBI")
ARATHA.NCBI.gff3.longest$genepos
ARATHA.NCBI.gff3.longest$cds
## set ENSEMBL GFF3 URL
ensembl <- "http://ftp.ensemblgenomes.org/pub/plants/release-52/"
ARATHA.ENSEMBL.gff3.url <- paste0(ensembl,
    "gff3/arabidopsis_thaliana/Arabidopsis_thaliana.TAIR10.52.gff3.gz")
ARATHA.ENSEMBL.gff3.file <- tempfile()
## download GTF file
download.file(ARATHA.ENSEMBL.gff3.url, ARATHA.ENSEMBL.gff3.file, quiet=FALSE)
## set ENSEMBL CDS URL
ARATHA.ENSEMBL.cds.url <- paste0(ensembl,
    "fasta/arabidopsis_thaliana/cds/",
    "Arabidopsis_thaliana.TAIR10.cds.all.fa.gz")
ARATHA.ENSEMBL.cds.file <- tempfile()
## download CDS file
download.file(ARATHA.ENSEMBL.cds.url, ARATHA.ENSEMBL.cds.file, quiet=FALSE)
ARATHA.ENSEMBL.cds <- Biostrings::readDNAStringSet(ARATHA.ENSEMBL.cds.file)
## get genepos and longest isoform
ARATHA.ENSEMBL.gff3.longest <- gff2longest(gff3file=ARATHA.ENSEMBL.gff3.file,
    cds=ARATHA.ENSEMBL.cds)
ARATHA.ENSEMBL.gff3.longest$genepos
ARATHA.ENSEMBL.gff3.longest$cds

## End(Not run)

---

gtf2longest

Description

This function extracts the gene position from GTF input and optional extracts the longest isoform.

Usage

gtf2longest(gtffile, cds = NULL, removeNonCoding = TRUE, source = "NCBI")

Arguments

gtffile	GTF path [mandatory]
cds	DNAStringSet [optional]
removeNonCoding	specify if NonCoding transcripts should be removed
source	source indicating either NCBI or ENSEMBL [default: NCBI]

Value

list

Author(s)

Kristian K Ullrich

See Also

XStringSet-class

Examples

## Not run: 
## load example sequence data
## set NCBI GTF URL
NCBI <- "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/"
ARATHA.NCBI.gtf.url <- paste0(NCBI,
    "GCF/000/001/735/GCF_000001735.4_TAIR10.1/",
    "GCF_000001735.4_TAIR10.1_genomic.gtf.gz")
ARATHA.NCBI.gtf.file <- tempfile()
## download GTF file
download.file(ARATHA.NCBI.gtf.url, ARATHA.NCBI.gtf.file, quiet=FALSE)
## set NCBI CDS URL
ARATHA.NCBI.cds.url <- paste0(NCBI,
    "GCF/000/001/735/GCF_000001735.4_TAIR10.1/",
    "GCF_000001735.4_TAIR10.1_cds_from_genomic.fna.gz")
ARATHA.NCBI.cds.file <- tempfile()
## download CDS file
download.file(ARATHA.NCBI.cds.url, ARATHA.NCBI.cds.file, quiet=FALSE)
## load CDS
ARATHA.NCBI.cds <- Biostrings::readDNAStringSet(ARATHA.NCBI.cds.file)
## get genepos and longest isoform
ARATHA.NCBI.gtf.longest <- gtf2longest(gtffile=ARATHA.NCBI.gtf.file,
    cds=ARATHA.NCBI.cds, source="NCBI")
ARATHA.NCBI.gtf.longest$genepos
ARATHA.NCBI.gtf.longest$cds
## set ENSEMBL GTF URL
ensembl <- "http://ftp.ensemblgenomes.org/pub/plants/release-52/"
ARATHA.ENSEMBL.gtf.url <- paste0(ensembl,
    "gtf/arabidopsis_thaliana/Arabidopsis_thaliana.TAIR10.52.gtf.gz")
ARATHA.ENSEMBL.gtf.file <- tempfile()
## download GTF file
download.file(ARATHA.ENSEMBL.gtf.url, ARATHA.ENSEMBL.gtf.file, quiet=FALSE)
## set ENSEMBL CDS URL
ARATHA.ENSEMBL.cds.url <- paste0(ensembl,
    "fasta/arabidopsis_thaliana/cds/",
    "Arabidopsis_thaliana.TAIR10.cds.all.fa.gz")
ARATHA.ENSEMBL.cds.file <- tempfile()
## download CDS file
download.file(ARATHA.ENSEMBL.cds.url, ARATHA.ENSEMBL.cds.file, quiet=FALSE)
ARATHA.ENSEMBL.cds <- Biostrings::readDNAStringSet(ARATHA.ENSEMBL.cds.file)
## get genepos and longest isoform
ARATHA.ENSEMBL.gtf.longest <- gtf2longest(gtffile=ARATHA.ENSEMBL.gtf.file,
    cds=ARATHA.ENSEMBL.cds)
ARATHA.ENSEMBL.gtf.longest$genepos
ARATHA.ENSEMBL.gtf.longest$cds

## End(Not run)

---

hom_pan_ensembl_kaks-data

Description

Example of Ka/Ks values between Homo sapiens and Pan troglodytes obtained from NCBI.

Usage

data(hom_pan_ensembl_kaks)

Format

an object of class list

Examples

data("hom_pan_ensembl_kaks", package="CRBHits")

---

isoform2longest

Description

This function extracts the longest isoform from either NCBI or ENSEMBL CDS input.

Usage

isoform2longest(cds, source = "NCBI")

Arguments

cds	DNAStringSet [mandatory]
source	source indicating either NCBI, ENSEMBL or WORMBASE [default: NCBI]

Value

DNAStringSet

Author(s)

Kristian K Ullrich

See Also

XStringSet-class

Examples

## Not run: 
## load example sequence data
## set NCBI URL
NCBI <- "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/"
HOMSAP.NCBI.cds.url <- paste0(NCBI,
    "GCF/000/001/405/GCF_000001405.39_GRCh38.p13/",
    "GCF_000001405.39_GRCh38.p13_cds_from_genomic.fna.gz")
HOMSAP.NCBI.cds.file <- tempfile()
## download CDS file
download.file(HOMSAP.NCBI.cds.url, HOMSAP.NCBI.cds.file, quiet=FALSE)
HOMSAP.NCBI.cds <- Biostrings::readDNAStringSet(HOMSAP.NCBI.cds.file)
## get longest isoform
HOMSAP.NCBI.cds.longest <- isoform2longest(HOMSAP.NCBI.cds, "NCBI")
length(HOMSAP.NCBI.cds)
length(HOMSAP.NCBI.cds.longest)
## set ENSEMBL URL
ensembl <- "ftp://ftp.ensembl.org/pub/release-101/fasta/"
## set Homo sapiens CDS URL
HOMSAP.ENSEMBL.cds.url <- paste0(ensembl,
    "homo_sapiens/cds/Homo_sapiens.GRCh38.cds.all.fa.gz")
HOMSAP.ENSEMBL.cds.file <- tempfile()
## download CDS file
download.file(HOMSAP.ENSEMBL.cds.url, HOMSAP.ENSEMBL.cds.file, quiet=FALSE)
HOMSAP.ENSEMBL.cds <- Biostrings::readDNAStringSet(HOMSAP.ENSEMBL.cds.file)
## get longest isoform
HOMSAP.ENSEMBL.cds.longest<-isoform2longest(HOMSAP.ENSEMBL.cds, "ENSEMBL")
length(HOMSAP.ENSEMBL.cds)
length(HOMSAP.ENSEMBL.cds.longest)

## End(Not run)

---

make_dagchainer

Description

This function tries to build the DAGchainer from source code forked within CRBHits

Usage

make_dagchainer(build_dir = file.path(find.package("CRBHits"), "extdata"))

Arguments

build_dir

directory to build DAGchainer [mandatory]

Value

compile DAGchainer and return binary path

Author(s)

Kristian K Ullrich

References

Haas BJ et al. (2004) DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics 20 (18), 3643-6.

---

make_last

Description

This function tries to build the prerequisite last-1639 from source code forked within CRBHits

Usage

make_last(build_dir = file.path(find.package("CRBHits"), "extdata"))

Arguments

build_dir

directory to build last [mandatory]

Value

compile last and return binary path

Author(s)

Kristian K Ullrich

References

Kiełbasa SM et al. (2011) Adaptive seeds tame genomic sequence comparison. Genome Res. 21 (3), 487-93.

---

make_vignette

Description

This function tries to build the prerequisite last-1639, and DAGchainer from source code forked within CRBHits

Usage

make_vignette()

Value

path of prerequisites

Author(s)

Kristian K Ullrich

References

Kiełbasa SM et al. (2011) Adaptive seeds tame genomic sequence comparison. Genome Res. 21 (3), 487-93.

Wang D, Zhang Y et al. (2010) KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genomics Proteomics Bioinformatics. 8(1), 77-80.

Haas BJ et al. (2004) DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics 20 (18), 3643-6.

---

plot_dagchainer

Description

This function plots DAGchainer (http://dagchainer.sourceforge.net/) results obtained via 'rbh2dagchainer()' function.

Usage

plot_dagchainer(
  dag,
  DotPlotTitle = "DAGchainer results",
  colorBy = "none",
  kaks = NULL,
  ka.max = 5,
  ks.max = 5,
  ka.min = 0,
  ks.min = 0,
  select.chr = NULL
)

Arguments

dag	specify DAGchainer results as obtained via 'rbh2dagchainer()' [mandatory]
DotPlotTitle	specify DotPlot title [default: DAGchainer results]
colorBy	specify if dagchainer groups should be colored by "Ka", "Ks", "Ka/Ks" or "none" [default: none]
kaks	specify Ka/Ks input obtained via 'rbh2kaks()' [default: NULL]
ka.max	specify max Ka to be filtered [default: 5]
ks.max	specify max Ks to be filtered [default: 5]
ka.min	specify min Ka to be filtered [default: 0]
ks.min	specify min Ks to be filtered [default: 0]
select.chr	filter results for chromosome names [default: NULL]

Value

synteny plot

Author(s)

Kristian K Ullrich

Examples

## load example sequence data
data("ath_aly_ncbi_dagchainer", package="CRBHits")
## plot DAGchainer results - default
plot_dagchainer(
    dag=ath_aly_ncbi_dagchainer)
## chromosome subset
plot_dagchainer(
    dag=ath_aly_ncbi_dagchainer,
    select.chr=c("NC_000932.1", "NC_034379.1"))

---

plot_kaks

Description

This function plots Ka/Ks results obtained via 'rbh2kaks()' function or 'MSA2dist::dnastring2kaks()' function.

Usage

plot_kaks(
  kaks,
  dag = NULL,
  gene.position.cds1 = NULL,
  gene.position.cds2 = NULL,
  tandem.dups.cds1 = NULL,
  tandem.dups.cds2 = NULL,
  PlotTitle = "Ka/Ks results",
  PlotType = "h",
  binw = 0.05,
  splitByChr = FALSE,
  colorBy = "none",
  ka.max = 5,
  ks.max = 5,
  ka.min = 0,
  ks.min = 0,
  select.chr = NULL,
  doPlot = TRUE
)

Arguments

kaks	specify Ka/Ks input obtained via 'rbh2kaks()' [mandatory]
dag	specify DAGchainer results as obtained via 'rbh2dagchainer()' [default: NULL]
gene.position.cds1	specify gene position for cds1 sequences (see cds2genepos) [default: NULL]
gene.position.cds2	specify gene position for cds2 sequences (see cds2genepos) [default: NULL]
tandem.dups.cds1	specify tandem duplicates for cds1 sequences (see tandemdups) [default: NULL]
tandem.dups.cds2	specify tandem duplicates for cds2 sequences (see tandemdups) [default: NULL]
PlotTitle	specify Plot title [default: Ka/Ks results]
PlotType	specify Plot type: "h" histogram or "d" dotplot [default: h]
binw	specify binwidth (see geom_histogram) [default: 0.05]
splitByChr	specify if plot should be split by chromosome [default: FALSE]
colorBy	specify if Ka/Ks gene pairs should be colored by "rbh_class", "dagchainer", "tandemdups" or "none" [default: rbh_class]
ka.max	specify max Ka to be filtered [default: 5]
ks.max	specify max Ks to be filtered [default: 5]
ka.min	specify min Ka to be filtered [default: 0]
ks.min	specify min Ks to be filtered [default: 0]
select.chr	filter results for chromosome names [default: NULL]
doPlot	specify plot [default: TRUE]

Value

Ka/Ks plot

Author(s)

Kristian K Ullrich

Examples

## load example sequence data
data("ath_aly_ncbi_kaks", package="CRBHits")
## plot Ka/Ks values - default
g <- plot_kaks(ath_aly_ncbi_kaks)
## Calculate Ka/Ks values based on MSA
data("hiv", package="MSA2dist")
hiv_kaks <- MSA2dist::dnastring2kaks(hiv)
g <- plot_kaks(hiv_kaks)

---

rbh2dagchainer

Description

This function runs DAGchainer (http://dagchainer.sourceforge.net/) given CRBHit pairs and gene positions for both cds1 and cds2. The default options are set to not compare gene positions in base pairs but instead using gene order (gene.idx).

Usage

rbh2dagchainer(
  rbhpairs,
  selfblast1 = NULL,
  selfblast2 = NULL,
  gene.position.cds1 = NULL,
  gene.position.cds2 = NULL,
  dagchainerpath = file.path(find.package("CRBHits"), "extdata", "dagchainer"),
  gap_open_penalty = 0,
  gap_extension_penalty = -3,
  gap_length = 10000,
  max_match_score = 50,
  max_dist_allowed = 2e+05,
  max_evalue = 0.001,
  ignore_tandem = TRUE,
  only_tandem = FALSE,
  min_number_aligned_pairs = 5,
  type = "bp",
  plotDotPlot = FALSE,
  DotPlotTitle = "DAGchainer results",
  colorBy = "none",
  kaks = NULL,
  ka.max = 5,
  ks.max = 5,
  ka.min = 0,
  ks.min = 0,
  select.chr = NULL
)

Arguments

rbhpairs	(conditional-)reciprocal best hit (CRBHit) pair result (see cds2rbh) [mandatory]
selfblast1	(conditional-)reciprocal best hit (CRBHit) pair selfblast result for cds1 sequences (see cds2rbh) [optional]
selfblast2	(conditional-)reciprocal best hit (CRBHit) pair selfblast result for cds2 sequences (see cds2rbh) [optional]
gene.position.cds1	specify gene position for cds1 sequences (see cds2genepos) [default: NULL]
gene.position.cds2	specify gene position for cds2 sequences (see cds2genepos) [default: NULL]
dagchainerpath	specify the PATH to the DAGchainer directory containing the dagchainer binaries [default: /extdata/dagchainer/]
gap_open_penalty	gap open penalty [default: 0]
gap_extension_penalty	gap extension penalty [default: -3]
gap_length	length of a gap (avgerage distance expected between two syntenic genes); if type is set to "idx" use 1 [default: 10000]
max_match_score	Maximum match score [default: 50]
max_dist_allowed	maximum distance allowed between two matches; if type is set to "idx" use 20 [default: 200000]
max_evalue	Maximum E-value [default: 1e-3]
ignore_tandem	ignore tandem duplicates [default = TRUE]
only_tandem	only tandem alignments [default = FALSE]
min_number_aligned_pairs	Minimum number of Aligned Pairs [default: 5]
type	specify if gene order index "idx" or gene base pair position "bp" should be extracted and used with DAGchainer [default: bp]
plotDotPlot	specify if dotplot should be plotted [default: FALSE]
DotPlotTitle	specify DotPlot title [default: 'DAGchainer results']
colorBy	specify if dagchainer groups should be colored by "Ka", "Ks", "Ka/Ks" or "none" [default: none]
kaks	specify Ka/Ks input obtained via 'rbh2kaks()' [default: NULL]
ka.max	specify max Ka to be filtered [default: 5]
ks.max	specify max Ks to be filtered [default: 5]
ka.min	specify min Ka to be filtered [default: 0]
ks.min	specify min Ks to be filtered [default: 0]
select.chr	filter results for chromosome names [default: NULL]

Value

DAGchanier results
1: $gene1.chr
2: $gene1.seq.id
3: $gene1.start
4: $gene1.end
5: $gene1.mid
6: $gene1.idx
7: $gene2.chr
8: $gene2.seq.id
9: $gene2.start
10: $gene2.end
11: $gene2.mid
12: $gene2.idx
13: $evalue
14: $score

Author(s)

Kristian K Ullrich

References

Haas BJ et al. (2004) DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics. 20(18), 3643-3646.

See Also

plot_dagchainer, cds2genepos, tandemdups, rbh2kaks

Examples

## compile dagchainer
CRBHits::make_dagchainer()
## load example sequence data
data("ath", package="CRBHits")
## get selfhits CRBHit pairs
ath_selfhits_crbh <- cds2rbh(
    cds1=ath,
    cds2=ath,
    plotCurve=TRUE)
## get gene position
ath.genepos <- cds2genepos(
    cds=ath,
    source="ENSEMBL")
## get DAGchainer results
ath_selfblast_crbh.dagchainer <- rbh2dagchainer(
    rbhpairs=ath_selfhits_crbh,
    gene.position.cds1=ath.genepos,
    gene.position.cds2=ath.genepos)
head(ath_selfblast_crbh.dagchainer)
## plot dagchainer
plot_dagchainer(
    dag=ath_selfblast_crbh.dagchainer)

---

rbh2kaks

Description

This function calculates Ka/Ks (dN/dS; accoring to Li (1993) or Yang and Nielson (2000) for each (conditional-)reciprocal best hit (CRBHit) pair. The names of the rbh columns must match the names of the corresponding cds1 and cds2 DNAStringSet vectors.

Usage

rbh2kaks(
  rbhpairs,
  cds1,
  cds2,
  model = "Li",
  plotHistPlot = FALSE,
  plotDotPlot = FALSE,
  dag = NULL,
  gene.position.cds1 = NULL,
  gene.position.cds2 = NULL,
  tandem.dups.cds1 = NULL,
  tandem.dups.cds2 = NULL,
  colorBy = "none",
  threads = 1,
  ...
)

Arguments

rbhpairs	(conditional-)reciprocal best hit (CRBHit) pair result (see cds2rbh) [mandatory]
cds1	cds1 sequences as DNAStringSet or url for first crbh pairs column [mandatory]
cds2	cds2 sequences as DNAStringSet or url for second crbh pairs column [mandatory]
model	specify codon model either "Li" or "NG86" or one of KaKs_Calculator2 model "NG", "LWL", "LPB", "MLWL", "MLPB", "GY", "YN", "MYN", "MS", "MA", "GNG", "GLWL", "GLPB", "GMLWL", "GMLPB", "GYN", "GMYN" [default: Li]
plotHistPlot	specify if histogram should be plotted [default: TRUE]
plotDotPlot	specify if dotplot should be plotted (mandatory to define gene.position.cds1 and gene.position.cds1) [default: FALSE]
dag	specify DAGchainer results as obtained via 'rbh2dagchainer()' [default: NULL]
gene.position.cds1	specify gene position for cds1 sequences (see cds2genepos) [default: NULL]
gene.position.cds2	specify gene position for cds2 sequences (see cds2genepos) [default: NULL]
tandem.dups.cds1	specify tandem duplicates for cds1 sequences (see tandemdups) [default: NULL]
tandem.dups.cds2	specify tandem duplicates for cds2 sequences (see tandemdups) [default: NULL]
colorBy	specify if Ka/Ks gene pairs should be colored by "rbh_class", dagchainer", "tandemdups" or "none" [default: none]
threads	number of parallel threads [default: 1]
...	other codon alignment parameters (see cds2codonaln) and other plot_kaks parameters (see plot_kaks)

Value

Ka/Ks values

Author(s)

Kristian K Ullrich

References

Li WH. (1993) Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol., 36, 96-99.

Wang D, Zhang Y et al. (2010) KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genomics Proteomics Bioinformatics. 8(1), 77-80.

Yang Z and Nielson R. (2000) Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol., 17(1), 32-43.

See Also

dnastring2kaks, isoform2longest, cds2genepos, plot_kaks, rbh2dagchainer, tandemdups

Examples

## load example sequence data
data("ath", package="CRBHits")
data("aly", package="CRBHits")
## load example CRBHit pairs
data("ath_aly_crbh", package="CRBHits")
## only analyse subset of CRBHit pairs
ath_aly_crbh$crbh.pairs <- head(ath_aly_crbh$crbh.pairs)
ath_aly_crbh.kaks <- rbh2kaks(
    rbhpairs=ath_aly_crbh,
    cds1=ath,
    cds2=aly,
    model="Li")
head(ath_aly_crbh.kaks)
## plot kaks
g.kaks <- plot_kaks(ath_aly_crbh.kaks)

---

seqid

Description

This function returns the first whitespace separated names value of a XStringSet.

Usage

seqid(x)

Arguments

x	XStringSet [mandatory]

Value

chr

Author(s)

Kristian K Ullrich

Examples

## load example sequence data
data("ath", package="CRBHits")
seqid(ath)

---

tandemdups

Description

This function assigns tandem duplicates given (conditional-)reciprocal best hit (CRBHit) pairs and their chromosomal gene position. The function is ported into R from Haug-Baltzell et al. (2017) https://github.com/LyonsLab/coge/blob/master/bin/dagchainer/tandems.py

Usage

tandemdups(rbhpairs, genepos, dupdist = 5)

Arguments

rbhpairs	(conditional-)reciprocal best hit (CRBHit) pair result (see cds2rbh) [mandatory]
genepos	Gene position matrix as obtained from cds2genepos [mandatory]
dupdist	Maximum distance between 2 gene positions on the same chromosome which will call them as a pair of local duplicates. If they are farther apart than dupdist, but share a common hit within dupdist of both, then they will still be in the same set of local duplicates. [default: 5]

Value

matrix 1: $gene.seq.id
2: $gene.chr
3: $gene.start
4: $gene.end
5: $gene.mid
6: $gene.strand
7: $gene.idx
8: $tandem_group

Author(s)

Kristian K Ullrich

References

Haug-Beltzell A et al. (2017) SynMap2 and SynMap3D: web-based whole-genome synteny browsers. Bioinformatics 33(14), 2197-2198.

See Also

isoform2longest

Examples

## load example sequence data
data("ath", package="CRBHits")
## get selfhits CRBHit pairs
ath_selfhits_crbh <- cds2rbh(
    cds1=ath,
    cds2=ath,
    plotCurve=TRUE)
## get gene position
ath.genepos <- cds2genepos(
    cds=ath,
    source="ENSEMBL")
## get tandem duplicate results
ath_selfblast_crbh.tandemdups <- tandemdups(
    rbhpairs=ath_selfhits_crbh,
    genepos=ath.genepos)
head(ath_selfblast_crbh.tandemdups)

---