sampleOverlap {MOMA} | R Documentation

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

### 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

[Package MOMA version 1.2.0 Index]