rbh2dagchainer: rbh2dagchainer

In kullrich/CRBHits: Conditional reciprocal best hits (CRBHits) in R

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 = paste0(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 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)

kullrich/CRBHits documentation built on Nov. 13, 2024, 7:44 a.m.