collate_bb_subclones: This function takes a Battenberg styled data.frame, pulls out...

In shaghayeghsoudi/DPclust3p_Customised: Dirichlet Process Clustering Pre-Processing Package

This function takes a Battenberg styled data.frame, pulls out the A copy number profile, then it calculates the total CN and a weighted ploidy before it subsets the input data by columns: "chr", "startpos", "endpos", "nMaj1_A", "nMin1_A", "frac1_A", "nMaj2_A", "nMin2_A", "frac2_A", "SDfrac_A".

Description

Then logic is applied for classifying copy number aberrations into a series of classes. There are two main groups: Clonal (starting with c) and Subclonal (starting with s).

Usage

collate_bb_subclones(
  samplename,
  cndata,
  gender,
  outfile,
  ploidy = NA,
  exclude_sex_chroms = F
)

Arguments

samplename	A String containing the samplename
cndata	A data.frame in Battenberg subclones format
gender	Specify either the string male or female
outfile	A String with the full path to where the output should be written
ploidy	An optional parameter that is used to call gains/losses against. If higher than the ploidy a segment is considered a gain, lower a loss. When left as NA the sample ploidy is used (Default NA).
exclude_sex_chroms	Optional parameter whether to exclude sex chromosomes (Default FALSE)

Details

A CNA can be: * HD : Homozygous deletion * LOH : Loss of heterozygosity * Amp : Amplification * Gain : Gain * NoCNV : Normal copy number without aberrations * Loss : Loss

The copy number segments, classification, weighted ploidy and samplename are saved to the specified output file

Author(s)

tjm

shaghayeghsoudi/DPclust3p_Customised documentation built on March 18, 2022, 5:28 a.m.