associateEvents: Use 'aREA' to calculate the enrichment between each genomic...

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

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)

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