overlapGenes: Calculates Genes that overlap the SV region

In nanotatoR: nanotatoR: next generation structural variant annotation and classification

Description

Calculates Genes that overlap the SV region

Usage

overlapGenes(bed, chrom, startpos, endpos, svid)

Arguments

bed	Text Bionano Bed file.
chrom	character SVmap chromosome.
startpos	numeric starting position of the breakpoints.
endpos	numeric end position of the breakpoints.
svid	numeric Structural variant identifier (Bionano generated).

Value

Data Frame. Contains the SVID,Gene name,strand information and percentage of SV covered.

Examples

smapName="F1.1_TestSample1_solo_hg19.smap"
smap = system.file("extdata", smapName, package="nanotatoR")
bedFile <- system.file("extdata", "Homo_sapiens.Hg19.bed", 
 package="nanotatoR")
bed<-buildrunBNBedFiles(bedFile,returnMethod="dataFrame")
smap<-readSMap(smap)
chrom<-smap$RefcontigID1
startpos<-smap$RefStartPos
endpos<-smap$RefEndPos
if (length(grep("SVIndex",names(smap)))>0){
   svid <- smap$SVIndex
 }else{
 svid <- smap$SmapEntryID
 }
overlapGenes(bed, chrom, startpos, endpos, svid)

nanotatoR documentation built on Nov. 8, 2020, 6:54 p.m.