overlapGenes {nanotatoR} | R Documentation |
Calculates Genes that overlap the SV region
overlapGenes( bed, chrom, startpos, endpos, svid, chrom2, SVTyp, bperrorindel = 3000, bperrorinvtrans = 50000 )
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). |
chrom2 |
character SVmap chromosome number 2. |
SVTyp |
Character. Type of SV. |
bperrorindel |
Numeric. base pair error indel. |
bperrorinvtrans |
Numeric. base pair error invtranslocation. |
Data Frame. Contains the SVID,Gene name,strand information and percentage of SV covered.
smapName="GM24385_Ason_DLE1_VAP_trio5.smap" smap = system.file("extdata", smapName, package="nanotatoR") bedFile <- system.file("extdata", "HomoSapienGRCH19_lift37.bed", package="nanotatoR") bed<-buildrunBNBedFiles(bedFile,returnMethod="dataFrame") smap<-readSMap_DLE(smap, input_fmt_smap = "Text") chrom<-smap$RefcontigID1 chrom2 <- smap$RefcontigID2 startpos<-smap$RefStartPos endpos<-smap$RefEndPos if (length(grep("SVIndex",names(smap)))>0){ svid <- smap$SVIndex }else{ svid <- smap$SmapEntryID } SVTyp <- smap$Type overlapGenes(bed = bed, chrom = chrom, startpos = startpos, endpos = endpos, chrom2 = chrom2, svid = svid, SVTyp = SVTyp, bperrorindel = 3000, bperrorinvtrans = 50000)