getStories: Combines variants and CNAs to clonal evolution

In ChristofferFlensburg/superFreq: Calls and tracks CNAs, SNVs and clones over multiple cancer exomes.

Combines variants and CNAs to clonal evolution

Description

Combines variants and CNAs to clonal evolution

Usage

getStories(
  variants,
  cnvs,
  timeSeries,
  normals,
  genome,
  cloneDistanceCut = -qnorm(0.01),
  Rdirectory,
  plotDirectory,
  cpus = 1,
  forceRedo = F,
  manualStoryMerge = F,
  correctReferenceBias = T,
  rareGermline = T,
  maxStories = 3000
)

Arguments

variants	variants: The variants.
cnvs	cnvs: The copy number calls.
timeSeries	names list of vectors: samples to be analysed together, named by individual.
normals	named boolean vector: which sameples (names of vector) are normal.
genome	character: the genome.
Rdirectory	character: The save directory.
plotDirectory	character: the directory to plot to.
cpus	integer: maximum number of parallel processes. Default 1.
forceRedo	boolen: if redoing calculations even if saved data is available. Default FALSE.

Details

This function calls VEP on the output from outputSomaticVariants. For this, VEP needs to be callable by system('vep').

ChristofferFlensburg/superFreq documentation built on Nov. 15, 2023, 6:15 a.m.