tandemdups

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

References

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

Author

Kristian K Ullrich

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)
#> # A tibble: 6 × 8
#>   gene.seq.id gene.chr gene.start gene.end gene.mid gene.strand gene.idx
#>   <chr>       <chr>         <dbl>    <dbl>    <dbl> <chr>          <int>
#> 1 AT1G01130.1 1             61905    63811   62858  -1                13
#> 2 AT1G01140.1 1             64166    67774   65970  -1                14
#> 3 AT1G01390.2 1            148013   149848  148930. -1                41
#> 4 AT1G01420.2 1            154367   156178  155272. -1                44
#> 5 AT1G01580.2 1            208995   213082  211038. 1                 61
#> 6 AT1G01590.1 1            214150   217734  215942  1                 62
#> # ℹ 1 more variable: tandem_group <chr>