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

Description Usage Arguments Value

View source: R/genomic.saturation.r

Description

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

Usage

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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


MOMA documentation built on Nov. 8, 2020, 6:01 p.m.