buildCustomIncidenceMatrix: This function builds an incidence matrix for custom gene...

In attract: Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape

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.

attract documentation built on Nov. 8, 2020, 8:04 p.m.