generateCombinedReport: Generate a gene-level overview of all overlapping mutations...

In J0bbie/R2CPCT: Misc. functions to perform import and analysis of WGS and RNA-Seq samples

Description

The gene-level overview will be performed on a per-sample basis using only protein-coding genes. The combined report will only contain protein-coding genes which have at least a single somatic aberration or were detected in the dN/dS or GISTIC2 analysis.

Use the 'selectedGenes' parameter to retrieve your genes-of-interests, even if no aberrations were detected.

Usage

generateCombinedReport(
  data.Cohort,
  dNdS,
  GISTIC2,
  nThreads = 40,
  mutantsOnly = TRUE
)

Arguments

data.Cohort	(list): Cohort-wide data obtained from importWGSOfCohort.
dNdS	(list): Output of the dN/dS analysis obtained from rundNdS.
GISTIC2	(list): Output of the GISTIC2 analysis obtained from importGISTIC2.
nThreads	(integer): Number of cores over which to parallelize (when needed).
mutantsOnly	(logical): Only output records with mutations (CNA, LOH or Muts; TRUE) or return all records (FALSE).

Value

(tibble) Returns a per-sample gene-level overview of all reported somatic aberrations on protein-coding genes.

Author(s)

Job van Riet [e-mail]

Examples

	# Generate a combined gene-level report of an imported WGS cohort (which could be a subset).
	generateCombinedReport(data.Cohort, results.Cohort$dNdS, results.Cohort$GISTIC2)

J0bbie/R2CPCT documentation built on Feb. 24, 2022, 8:15 a.m.