momaConstructor: MOMA Constructor Function

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

Description

Create MOMA Object from either a MultiAssayExperiment object or a list of assays. See vignette for more information on how to set up and run the MOMA object

Usage

MomaConstructor(
  x,
  pathways,
  gene.blacklist = NA_character_,
  output.folder = NA_character_,
  gene.loc.mapping = gene.map,
  viperAssay = "viper",
  mutMat = "mut",
  cnvMat = "cnv",
  fusionMat = "fusion"
)

Arguments

x	A MultiAssayExerperiment object or list object with the following assays: (note: by default assays must have these exact names. Otherwise they can be changed using the viperAssay, mutMat, cnvMat and fusionMat parameters.) viper VIPER protein activity matrix with samples as columns and rows as protein IDs mut An indicator matrix (0/1) of mutation events with samples as columns and genes as rows cnv A matrix of CNV scores (typically SNP6 array scores from TCGA) with samples as columns and genes as rows fusion An indicator matrix (0/1) of fusion events with samples as columns and genes as rows
pathways	A named list of lists. Each named list represents interactions between proteins (keys) and their associated partners
gene.blacklist	A vector of genes to exclude from the analysis
output.folder	Location to store output and intermediate results
gene.loc.mapping	A data.frame of band locations and Entrez IDs
viperAssay	name associated with the viper assay in the assay object
mutMat	name associated with the mutation matrix in the assay object
cnvMat	name associated with the cnv matrix in the assay object
fusionMat	name associated with the fusion matrix in the assay object

Value

an instance of class Moma

Examples

momaObj <- MomaConstructor(example.gbm.mae, gbm.pathways)

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