rbh2dagchainer

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).

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

References

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

Author

Kristian K Ullrich

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)
#> [1] "/tmp/RtmpxTj3oB/temp_libpath292860497075/CRBHits/extdata/dagchainer/run_DAG_chainer.pl -i /tmp/Rtmp4VHf4v/file298027549e6f -o 0 -e -3 -g 10000 -M 50 -D 200000 -E 0.001 -A 5 -I -s"
head(ath_selfblast_crbh.dagchainer)
#>   gene1.chr gene1.seq.id gene1.start gene1.end gene1.mid gene1.idx gene2.chr
#> 1     AA1:1  AT1G05100.1     1469541   1470881   1470211       437     AA1:1
#> 2     AA1:1  AT1G05400.1     1584073   1585421   1584747       468     AA1:1
#> 3     AA1:1  AT1G05570.1     1647575   1659611   1653593       484     AA1:1
#> 4     AA1:1  AT1G06100.1     1851472   1853019   1852246       546     AA1:1
#> 5     AA1:1  AT1G06120.1     1855910   1857718   1856814       548     AA1:1
#> 6     AA1:1  AT1G06290.1     1922208   1926278   1924243       570     AA1:1
#>   gene2.seq.id gene2.start gene2.end gene2.mid gene2.idx   evalue score
#> 1  AT1G07150.2     2193941   2195798   2194870       654  1.1e-55    50
#> 2  AT1G06810.1     2091738   2092539   2092138       620  8.2e-67    67
#> 3  AT1G06490.2     1978378   1989409   1983894       588 1.0e-250    87
#> 4  AT1G06360.2     1938862   1940496   1939679       576 2.0e-200    80
#> 5  AT1G06350.1     1935227   1936841   1936034       575 7.2e-177   130
#> 6  AT1G06310.1     1926652   1930397   1928524       571 1.0e-250   162
#>    dagchainer_group
#> 1 AA1:1:AA1:1:1.rev
#> 2 AA1:1:AA1:1:1.rev
#> 3 AA1:1:AA1:1:1.rev
#> 4 AA1:1:AA1:1:1.rev
#> 5 AA1:1:AA1:1:1.rev
#> 6 AA1:1:AA1:1:1.rev
## plot dagchainer
plot_dagchainer(
    dag=ath_selfblast_crbh.dagchainer)
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.

Arguments

Value

References

See also

Author

Examples