prepSupMoa: Prepare sumpplementary tables for projection by sup.moa or...

In mengchen18/mogsa: Multiple omics data integrative clustering and gene set analysis

Description

Convert a list of gene set information to a set of sumpplementary tables that can be used as input of function "sup.moa" or "mogsa".

Usage

prepSupMoa(X, geneSets, minMatch = 10, maxMatch = 500)

Arguments

X	A matrix/data.frame or a list of matrix/data.frame or a list of character vector. If it is a list of matrix/data.frame, row names of matrix/data.frame will be used to create the projection matrix. Otherwise the charater vectors will used to create the supplementary matirx.
geneSets	Gene sets list or an object of class "GeneSet" or "GeneSetCollection". A gene set list could be returned by prepGraphite or prepMolsigDB.
minMatch	The minimum match of geneset.
maxMatch	The maximum match genesets.

Details

Details here

Value

A list of matrix could used as supplementary tables by "sup.moa" or "mogsa".

Author(s)

Chen Meng

See Also

See Also as prepGraphite and prepMsigDB.

Examples

  library(graphite)
  data(NCI60_4arrays)
  kegg <- pathways(species = "hsapiens", "kegg")
  pw <- c("Purine metabolism", "MAPK signaling pathway")
  gss <- prepGraphite(db = kegg[pw], id="symbol")
  gss <- lapply(gss, function(x) sub("SYMBOL:", "", x))
  sup_data1 <- prepSupMoa(NCI60_4arrays, geneSets=gss)
  gene_list <- lapply(NCI60_4arrays, rownames)
  sup_data2 <- prepSupMoa(gene_list, geneSets=gss)

mengchen18/mogsa documentation built on June 7, 2020, 6:05 p.m.