NEWS

YAPSA 1.26.7

Some URLs are reformatted in the documentations and vignettes.
Data is only loaded into the function environment with 'data(..., envir = environment())'.
Namespace imports are adjusted to fixed the function name conflict.

We comply with changes in upstream dependency: PMCMR is replaced by PMCMRplus and consecutively the function posthoc.kruskal.nemenyi.test.default() is replaced by kwAllPairsNemenyiTest(). Also, in the package description, the syntax for authors and maintainers is adapted to current requirements of BiocCheck.

We provide a new function LCD_extractCohort_callPerPID() which also belongs to the LCD family and which performs the detection of signatures at cohort-wide level, but re-runs the actual computation of the exposures per-PID with only the signatures identified in the cohort-wide calling. The ovall wrapper function LCD_complex_cutoff_combined() now also calls the new function and stores the result in the returned list with item name extractCohort_callPerPID

Introduction of an input parameter minimumNumberOfAlterations for the functions LCD_complex_cutoff_perPID(), LCD_complex_cutoff_consensus() and LCD_complex_cutoff_combined(). If a sample has less mutations than this cutoff, a warning is issued. By default, this values is set to 25 and may be a good choice for analysis of SNV mutational signatures. For analysis of Indel mutational signatures, a better choice is 20.

95% Confidence intervals for exposures to mutational signatures can be computed
Analysis of the PCAWG mutational signatures is supported, both for PCAWG SNV and PCAWG Indel signatures

new vignettes have been written for the new features confidence intervals and Indel signatures
new vignettes were added for features already present in the package before, especially the optimal signature-specific cutoffs
the topic of stratifiec analyses of mutational signatures was taken out of the main vignette and now is described in a vignette on its own.