TitanCNA v1.17.1

TitanCNA version 1.17.1 changes

1. New functions:

   • correctIntegerCN(): recomputes high-level copy number that is capped by the maximum CN state.
     Performs two tasks - (1) correct log ratio based on purity and ploidy, and then convert to decimal CN value; (2) Correct bins and segments in which the original predicted integer copy number was assigned the maximum CN state; bins and segments for all of chromosome X are also corrected, if provided in the input.

2. Modified functions:

   • plotSegmentMedians() and plotCNlogRByChr(): includes argument to show color-coding for corrected copy number; defaults to TRUE for this argument.

3. Removed functions/manual/dependencies:

   • extractAlleleReadCounts()
   • Rsamtools dependency

Reminder:
A snakemake is also provided in this repo.
This workflow will run the TITAN a set of tumour-normal pairs, starting from the BAM files and generating TitanCNA outputs. It will also perform model selection at the end of the workflow to choose the optimal ploidy and clonal cluster solutions.