prepSupMoa: Prepare sumpplementary tables for projection by sup.moa or...
In mogsa: Multiple omics data integrative clustering and gene set analysis

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

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".

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

`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 here

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

Chen Meng

See Also as prepGraphite and prepMsigDB.

  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)