associateEvents {MOMA}R Documentation

Use 'aREA' to calculate the enrichment between each genomic event - VIPER inferred protein pair.

Description

Requires pre-computed VIPER scores and a binary events matrix. Will use only samples in both event and VIPER matrices.

Usage

associateEvents(
  vipermat,
  events.mat,
  min.events = NA,
  whitelist = NA,
  event.type = c("Amplifications", "Deletions", "Mutations", "Fusions", NA),
  verbose
)

Arguments

vipermat

Pre-computed VIPER scores with samples as columns and proteins as rows

events.mat

Binary 0/1 events matrix with samples as columns and genes or events as rows

min.events

Only compute enrichment if the number of samples with these events is GTE to this

whitelist

Only compute associations for events in this list

event.type

Name of the event type being analyzed

verbose

whether to print extra progress statements

Value

A matrix of aREA scores, dimensions are nrow(events.mat) x nrow(vipermat)

[Package MOMA version 1.0.2 Index]