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

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/preGeneSet.R

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

1
    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

1
2
3
4
5
6
7
8
9
  library(graphite)
  data(NCI60_4arrays)
  kegg <- pathways(species = "hsapiens", "kegg")
  pw <- c("Purine metabolism", "Endocrine resistance", "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 Nov. 23, 2017, 1:57 a.m.