buildCustomIncidenceMatrix {attract} | R Documentation

## This function builds an incidence matrix for custom gene sets.

### Description

This function builds an incidence matrix for custom gene sets.

### Usage

    buildCustomIncidenceMatrix(geneSetFrame, geneNames, databaseGeneFormat, expressionSetGeneFormat,geneSetNames)

### Arguments

`geneSetFrame` | a `dataframe` where rows are gene sets and columns are genes.
`geneNames` | a `vector` of all the genes in the geneSetFrame `dataframe`
`databaseGeneFormat` | a character string specifying the type of identifier for a gene in a database (KEGG, reactome, MsigDB) gene set. The default value is NULL. (ex. SYMBOL, ENTREZID, REFSEQ, ENSEMBL)
`expressionSetGeneFormat` | a character string specifying the type of identifier for a gene in your expression data set. The default value is NULL. (ex. SYMBOL, ENTREZID, REFSEQ, ENSEMBL)
`geneSetNames` | a `vector` of the name of the custom gene sets.

### Details

This function creates an incidence matrix from a dataframe where the rows are the names of gene sets and the columns are genes.

### Value

A matrix object with 0 and 1 entries where 1 denotes membership of a gene in a custom gene set, 0 denotes non-membership.

### Author(s)

Jessica Mar

### References

Mar, J., C. Wells, and J. Quackenbush, Identifying the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape. to appear, 2010.

[Package attract version 1.42.0 Index]