WES.Bin: Computes the read depth of a pair of BAM files and bins it.

In gustaveroussy/EaCoN: EaCoN : Easy Copy Number !

Description

This function computes the read depth of a pair of BAM files (typicaly tumor and normal) and bins it thanks to a "BINpack" generated with BINpack.Maker().

Usage

WES.Bin(testBAM = NULL, refBAM = NULL, BINpack = NULL, samplename = "SAMPLE",
Q = 20, nsubthread = 1, cluster.type = "PSOCK", out.dir = getwd(),
return.data  = FALSE, write.data = TRUE, plot = TRUE, force = FALSE)

Arguments

testBAM	BAM file corresponding to the tested sample (typically a patient tumor sample).
refBAM	BAM file corresponding to the reference sample (typically a patient normal sample).
BINpack	A data pack generated with EaCoN.BINpack.Maker() containing to a binned version of the capture BED used to generate the BAM files, and corresponding precomputed GC% tracks.
samplename	The name of the sample.
Q	Minimum baseQ/BAQ quality score as defined by samtools mpileup.
nsubthread	Number of subthreads for multithreading.
cluster.type	Type of subthreading cluster (see ?parallel::makeCluster()).
out.dir	Output directory.
return.data	Return the results.
write.data	Write the results as a RDS file.
plot	Perform plots.
force	If some result files already exist, delete them before runing.

Value

A RDS object containing binned read depths and SNP depths. If return.data is set to TRUE, its content is also returned.

Author(s)

Bastien Job

gustaveroussy/EaCoN documentation built on Oct. 20, 2021, 2:41 a.m.