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

Description Usage Arguments Value Author(s)

View source: R/wes_process.R

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

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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.