overlapGenes {nanotatoR}R Documentation

Calculates Genes that overlap the SV region

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)

[Package nanotatoR version 1.0.0 Index]