tandemdups: tandemdups

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

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)

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