Description Usage Arguments Value Note See Also Examples
View source: R/SCANVISlinkvar.R
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
1 | SCANVISlinkvar(scn, bed, gen, p = 0)
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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) |
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)
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.
SCANVISscan, SCANVISannotation, SCANVISvisual
1 2 3 4 5 6 7 8 9 10 | 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'])
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