readCNAProfile: Read CNA Profiles

In qingjian1991/MPTevol: Clonal Evolutionary History and Metastatic Routines Analysis for Multiple Primary Tumors

Read CNA Profiles

Description

We used a CNAqc object, containing a set of mutations, CNA calls and tumor purity values. The CNAqc was used to deal with the allele-specific CNAs.

Usage

readCNAProfile(maf, seg, Patient_ID = NULL, purity = 1, ref = "hg19")

Arguments

maf	Maf or MafList object generated by readMaf() function
seg	seg or seglist.
Patient_ID	Patient_ID: select the specific patients. IF not indicate, the input is Maf and seg, or the input is MafList and segList.
purity	purity information for each samples.
ref	human reference genome version. Default 'hg19'. Optional: 'hg18' or 'hg38'.

Details

This code reads the CNA Profiles for each patient. The tumor names of maf and seg are required to match each other.

Value

cnaqc.list for cnaqc initiation.

qingjian1991/MPTevol documentation built on Jan. 30, 2023, 10:16 p.m.