sampleOverlap {MOMA} | R Documentation |
The core function to compute which sample-specific alterations overlap with genomic events that are explained via DIGGIT.
sampleOverlap( MomaObject, viper.samples, selected.tfs, interaction.map, cnv.threshold = 0.5, mutation.filter = NULL, idx.range = NULL, verbose = FALSE )
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) |
A list of lists, indexed by sample name, with coverage statistics/data for each sample