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TitanCNA v1.13.1 release
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@gavinha gavinha released this 20 Jan 13:28
· 248 commits to master since this release
v1.13.1
8323cb7

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.

  1. 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).

  1. 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.

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