SCANVISlinkvar: maps variants to SCANVISscored junctions

In nygenome/SCANVIS: SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions

Description

This function maps variants to SJs by overlapping the union of gene coordinates that harbor the SJs (optionally, with some gene interval expansion) with variant coordinates

Usage

	SCANVISlinkvar(scn, bed, gen, p = 0)

Arguments

scn	matrix output by SCANVISscan
bed	matrix with variants in bed format with colnames chr, start, end and with and additional description column (eg. ssSNP for splice site mutations)
gen	gencode object as generated by the function SCANVISannotation
p	expands gene intervals up/downstream by p (default=0, no padding)

Value

Returns the input scn matrix with an additional column showing variants, if any, that occur in/near the listed genes. For instances where multiple variants map to a SJ, the variants are | separated (eg. chr7:145562;A>G|chr7:145592;C>G)

Note

The reference genome used to align RNA-seq reads that generated the initial set of SJs should be the same reference genome used for the variant calls.

See Also

SCANVISscan, SCANVISannotation, SCANVISvisual

Examples

data(SCANVISexamples)
gbm3.scn<-SCANVISscan(sj=gbm3,gen=gen19,Rcut=5)
### Variant format required (these are toy variants)
head(gbm3.vcf) 
gbm3.scnv<-SCANVISlinkvar(gbm3.scn,gbm3.vcf,gen19)
table(gbm3.scnv[,'passedMUT'])
### Expand variant intervals by p
gbm3.scnvp<-SCANVISlinkvar(gbm3.scn,gbm3.vcf,gen19,p=100)
### Observe variant chr6:46820148;Z>AA which was not previously matched to any SJ
table(gbm3.scnvp[,'passedMUT'])

nygenome/SCANVIS documentation built on July 19, 2019, 4:57 a.m.