correctLog2_ascat: ascat.correctLogR

In TearsWillFall/ULPwgs: An implementation of a wrapper for estimating tumor fraction in ultra-low-pass whole genome sequencing (ULP-WGS) for cell-free DNA in GNU/Unix based systems

ascat.correctLogR

Description

Corrects logR of the tumour sample(s) with genomic GC content (replication timing is optional)

Usage

correctLog2_ascat(
  ASCATobj,
  GCcontentfile = NULL,
  replictimingfile = NULL,
  threads = 4
)

Arguments

ASCATobj	an ASCAT object
GCcontentfile	File containing the GC content around every SNP for increasing window sizes
replictimingfile	File containing replication timing at every SNP for various cell lines (optional)

Details

Note that probes not present in the GC content file will be lost from the results

Value

ASCAT object with corrected tumour logR

TearsWillFall/ULPwgs documentation built on April 18, 2024, 3:45 p.m.