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.

TitanCNA version 1.15.0 changes

1. 10X Genomics analysis

• Please see scripts for instructions on running the 10X Genomics analysis.

2. New script to help select optimal solutions. Please see scripts/R_scripts

3. Added snakemake pipeline for entire TITAN workflow. Please see scripts/snakemake.

4. New function

• plotSegmentMedians()
• loadHaplotypeAlleleCounts(): loads input allele counts with phasing information
• plotHaplotypeFraction(): results from 10X Genomics WGS data with phasing of haplotype blocks

5. Modified features (no changes for user-accessible functions)

• updateParameters: coordinate descent estimate of ploidy update uses previously estimated normal parameter from the same corodinate descent iteration ; leads to faster convergence

TitanCNA version 1.13.1 changes

Note: Changed to v1.13.1 from v1.10.1 to match Bioconductor versioning

1. New function

outputTitanSegments:

Replaces the need for external Perl script to generate segments file.

2. Modified function

setupClonalParameters

Initializes cellular prevalence values evenly distributed between 0 and 1 rather than 0.1 increments.

loadDefaultParameters

added hetBaselineSkew argument which will determine the baseline allelic fraction to use. If this is NULL, then will set using the median allelic ratio across the genome ("data" argument). If "data" argument is NULL, then will simply set to 0.55 (heterozgyous skew of 0.05). Note that the "skew" argument applies to all other states except for the heterozygous allelic states (e.g. 1:1, 2:2, 3:3, 4:4 - for minor:major copies).

3. Bug fixes

plotClonalFrequency

Handle case when result is completely copy neutral heterozygous and cellular prevalence and ClonalClusters columns are both NA

runEMclonalCN

If EM ever decreases, then take last iteration (with higher likelihood).

filterData

Remove centromere positions now working.

TitanCNA version 1.7.1 changes (formerly v1.5.8)

Merged to master as v1.7.1 (a5bf4f3) (Committed revisions 977c48a,5fe5acc.)

1. Updated functions to align with dependent package updates.

   • Affected function: loadAlleleCounts, correctReadDepth
   • Adjusted function to accommodate GenomeInfoDb v1.1.3 -> v1.2.4
   • Usage of this function remains unchanged.

2. Minor bug fix in function

   • Affected function: correctReadDepth
   • Issue with findOverlaps() usage fixed

3. Bug fix

   • Affected function: outputTitanResults, plotClonalFrequency, plotSubcloneProfiles
   • Fixed bug when error is thrown trying to output results for genome that is predicted to be completely diploid HET.

4. Modified internal functionality

   • Affected function: runEMclonalCN, viterbiClonalCN
   • The C code (src/fwd_backC_clonalCN.c & src/viterbiC_clonalCN.c) have been modified such that the transition probabilities between clonal clusters for HET (diploid) states are equal. This may help prevent situations when normal contamination is 0 for more than 1 clonal cluster solutions.

TitanCNA v1.5.7 first release on GitHub

1. Fixed bug in utils.R, src/fwd_backC_clonalCN.c, and src/viterbiC_clonalCN.c
   • unfinished changes were accidentally committed in v1.5.6.
   • rolled "loadDefaultParameters" back to v1.5.5

For full list of changes for all versions, please refer to README.