Obtain BAF and LogR from the Cell line (tumour only) allele counts

Source: R/prepare_wgs_cell_line.R

Function to generate BAF and LogR files based on allele counts of the Cell line. It also generates the input data required by the following 'cell_line_reconstruct_normal' function.

cell_line_baf_logR(TUMOURNAME, g1000alleles.prefix, chrom_names)

Arguments

TUMOURNAME

The tumour name used for Battenberg (i.e. the cell line BAM file name without the '.bam' extension).

g1000alleles.prefix

Prefix to where 1000 Genomes allele files can be found.

chrom_names

A vector with allowed chromosome names.

Author

Naser Ansari-Pour (BDI, Oxford)