sampleOverlap: The core function to compute which sample-specific...

In califano-lab/MOMA: Multi Omic Master Regulator Analysis

Description

The core function to compute which sample-specific alterations overlap with genomic events that are explained via DIGGIT.

Usage

sampleOverlap(
  MomaObject,
  viper.samples,
  selected.tfs,
  interaction.map,
  cnv.threshold = 0.5,
  mutation.filter = NULL,
  idx.range = NULL,
  verbose = FALSE
)

Arguments

MomaObject	Object reference of momaRunner class
viper.samples	Sample vector to restrict sample-specific analysis to
selected.tfs	Transcription factors being analyzed
interaction.map	List object of events 'covered' by the supplied interactions of type mut/amp/del/fus
cnv.threshold	Numeric absolute value to threshold SNP6 and/or GISTIC or other CNV scores. Above that absolute value is considered a positive event.
mutation.filter	A vector of whitelisted mutation events, in entrez gene IDs
idx.range	Number of tfs to check for genomic saturation calculation, default is 1253
verbose	Output status during the run (default=FALSE)

Value

A list of lists, indexed by sample name, with coverage statistics/data for each sample

califano-lab/MOMA documentation built on June 7, 2020, 7:17 a.m.