overlapGenes {nanotatoR} | R Documentation |
Calculates Genes that overlap the SV region
overlapGenes(bed, chrom, startpos, endpos, svid)
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). |
Data Frame. Contains the SVID,Gene name,strand information and percentage of SV covered.
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)