generate.GC: generate.GC

In omicsCore/SEQprocess: SEQprocess : a modularized and customizable pipeline framework for NGS processing in R package.

Description

A wrapper function to run sequenza-utils.py in sequenza (GC-windows)

Usage

generate.GC(window=1,000,000, output.dir, ref.fa, run.cmd=TRUE)

Arguments

window	A parameter value for -w in sequenza. Indicate a window size (in bases), to be used for the binning. The heterozygous positions and the positions carrying variant calls are not affected by binning.
output.dir	Output directory
ref.fa	Reference fasta file path
run.cmd	Whether to execute the command line (default=TRUE)

Details

Calculation GC contents from reference fasta file

References

Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data.

See Also

https://cran.r-project.org/web/packages/sequenza/vignettes/sequenza.pdf

omicsCore/SEQprocess documentation built on May 7, 2020, 4:18 a.m.