| nonOverlapGenes {nanotatoR} | R Documentation |
Calculates Genes that are near to the SV region
nonOverlapGenes(bed, chrom, startpos, endpos, svid, n = 3)
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). |
n |
numeric Number of genes to report which are nearest to the breakpoint. Default is 3. |
Data Frame. Contains the SVID,Gene name,strand information and Distance from the 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
}
n<-3
nonOverlapGenes(bed, chrom, startpos, endpos, svid,n)