CreateReadsMatrix: CreateReadsMatrix

In ifCNVR: Isolation-Forest Based 'CNV' Detection from 'NGS' Data

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)

ifCNVR documentation built on March 18, 2022, 6:15 p.m.