GSNA (version 0.1.4.2)

makeFilteredGenePresenceAbsenceMatrix: makeFilteredGenePresenceAbsenceMatrix

Description

Take character vector containing the set of observable genes in a data set and a gene set collection and generate a presence/absence matrix of observable genes in each gene set/module.

Usage

makeFilteredGenePresenceAbsenceMatrix(ref.background, geneSetCollection)

Value

This returns a gene presence/absence matrix with genes corresponding to rows, gene sets/modules corresponding to columns, and TRUE or FALSE values corresponding to presence or absence of a particular gene in a particular gene set/module. This matrix has been filtered to only include genes observable in a data set.

Arguments

ref.background

(required) A character vector corresponding to the genes observable in a differential expression, ATAC-Seq or other dataset. This corresponds to the background used in tools like DAVID.

geneSetCollection

(required) A gene set collection either in the form of a tmod object, or a list of gene sets / modules as character vectors containing gene symbols and names corresponding to the gene module identifier.

See Also

buildGeneSetNetworkLFFast buildGeneSetNetworkSTLF buildGeneSetNetworkJaccard

Examples

library(GSNA)

# And obtain a background of observable genes from differential
# expression data:
background_genes <- toupper( rownames( Bai_CiHep_v_Fib2.de ) )

# Using Bai_gsc.tmod, the tmod format gene set collection in the
# sample data, we can now generate a filtered gene presence
# absence matrix. The columns of the matrix correspond to gene
# sets, whereas the rows are genes.
filteredGenePresenceAbsence_Matrix <-
          makeFilteredGenePresenceAbsenceMatrix( ref.background = background_genes,
                                                 geneSetCollection = Bai_gsc.tmod )