prepSupMoa {mogsa} | R Documentation

## Prepare sumpplementary tables for projection by sup.moa or mogsa.

### 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", "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)

[Package mogsa version 1.18.1 Index]