compSmapbed: Extracts gene information from bed files

Description Usage Arguments Value Examples

View source: R/Bed_SV_Comp.r

Description

Extracts gene information from bed files

Usage

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compSmapbed(smap, bed, inputfmtBed = c("BED", "BNBED"), outpath, n = 3,
  returnMethod_bedcomp = c("Text", "dataFrame"))

Arguments

smap

character. Path to SMAP file.

bed

Text. Normal Bed files or Bionano Bed file.

inputfmtBed

character Whether the bed input is UCSC bed or Bionano bed. Note: extract in bed format to be read by bedsv: awk 'print $1,$4,$5,$18,$7' gencode.v19.annotation.gtf>HomoSapienGRCH19.bed

outpath

character Path for the output files.

n

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

returnMethod_bedcomp

Character. Type of output Dataframe or in Text format.

Value

Data Frame and Text file. Contains the smap with additional Gene Information.

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_BN_bed.txt",
package="nanotatoR")
outpath <- system.file("extdata",  package="nanotatoR")
datcomp<-compSmapbed(smap, bed=bedFile, inputfmtBed =  "BNBED", n = 3, 
returnMethod_bedcomp = c("dataFrame"))
datcomp[1,]

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