nonOverlapGenes: Calculates Genes that are near to the SV region

In VilainLab/Nanotator: Next generation structural variant annotation and classification

Description

Calculates Genes that are near to the SV region

Usage

nonOverlapGenes(
  bed,
  chrom,
  startpos,
  chrom2,
  endpos,
  svid,
  n = 3,
  SVTyp,
  bperrorindel = 3000,
  bperrorinvtrans = 50000
)

Arguments

bed	Text Bionano Bed file.
chrom	character SVmap chromosome.
startpos	numeric starting position of the breakpoints.
chrom2	character SVmap 2nd chromosome.
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.
SVTyp	Character. Type of SV.
bperrorindel	Numeric. base pair error indel.
bperrorinvtrans	Numeric. base pair error invtranslocation.

Value

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

Examples

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
n<-3
nonOverlapGenes(bed = bed, chrom = chrom, startpos = startpos, 
endpos = endpos, svid = svid, chrom2 = chrom2, SVTyp = SVTyp,
   bperrorindel = 3000, bperrorinvtrans = 50000, n = 3)

VilainLab/Nanotator documentation built on Oct. 9, 2021, 8:59 p.m.