nonOverlapGenes: Calculates Genes that are near to the SV region

Description Usage Arguments Value Examples

View source: R/Bed_SV_Comp.r

Description

Calculates Genes that are near to the SV region

Usage

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nonOverlapGenes(bed, chrom, startpos, endpos, svid, n = 3)

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).

n

numeric Number of genes to report which are nearest to the breakpoint. Default is 3.

Value

Data Frame. Contains the SVID,Gene name,strand information and Distance from the SV covered.

Examples

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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)

VilainLab/Nanotator documentation built on May 20, 2019, 5:41 p.m.