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

Description Usage Arguments Details Value Author(s) References

View source: R/findAttractorsStep.R

Description

This function builds an incidence matrix for custom gene sets.

Usage

1
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.


jmarlab/attract documentation built on May 23, 2019, 9:02 p.m.