callChrXsubclones: Fit ChrX subclonal copy number (male only)

In Wedge-Oxford/battenberg: Battenberg subclonal copy number caller

Fit ChrX subclonal copy number (male only)

Description

Function to call ChrX copy number based on LogR (suitable for male samples). Copy number cannot be called for the non-PAR region of ChrX due to the hemizygosity of all 1000G SNPs. This function enables calling subclonal copy number for the non-PAR region by segmenting LogR. A number of correction steps are undertaken to account for the noisy nature of LogR. This function requires the following libraries: copynumber, data.table and ggplot2. It reads in three files generated by previous steps of Battenberg, namely TUMOURNAME_mutantLogR_gcCorrected.tab, TUMOURNAME_purity_ploidy.txt and TUMOURNAME_subclones.txt.

Usage

callChrXsubclones(
  TUMOURNAME,
  X_GAMMA = 1000,
  X_KMIN = 100,
  GENOMEBUILD,
  AR = TRUE
)

Arguments

TUMOURNAME	The tumour name used for Battenberg (i.e. the tumour BAM file name without the .bam extension)
X_GAMMA	The PCF gamma value for segmentation of 1000G SNP LogR values (Default 1000)
X_KMIN	The min number of SNPs to support a segment in PCF of LogR values (Default 100)
GENOMEBUILD	The genome build used in running Battenberg (hg19 or hg38)
AR	Should the segment carrying the androgen receptor (AR) locus to be visually distinguished in average plot? (Default TRUE)

Author(s)

Naser Ansari-Pour (BDI, Oxford)

Wedge-Oxford/battenberg documentation built on Aug. 4, 2023, 6:27 p.m.