CreateReadsMatrix {ifCNVR}

CreateReadsMatrix

Description

CreateReadsMatrix

Usage

CreateReadsMatrix(
  bamPath,
  bedFile,
  bedtoolsPath,
  outputFile = "n",
  verbose = TRUE
)

Arguments

bamPath

a path leading to the .bam and .bai files

bedFile

a path leading to the .bed file (Warning replace chrX by X in the position)

bedtoolsPath

the path leading to bedtools

outputFile

(optional) a path leading to a text file

verbose

a boolean

Value

a reads matrix

Examples

bamPath <- system.file("extdata/",package = "ifCNVR")
bed <- system.file("bedFile.bed",package = "ifCNVR")
bedtools <- 'n'
readsMatrix <- CreateReadsMatrix(bamPath, bed, bedtools)