filterGeneSets: Filter gene sets by size and presence of each gene in the...

In Mengbo-Li/brainClass: Transcriptional Data Guided fMRI Network Classification

Filter gene sets by size and presence of each gene in the reference gene expression data set

Description

The 'filterGeneSets' function filters gene sets by their sizes, and filters out genes not in the candidate list.

Usage

filterGeneSets(geneSetList, candidateGenes, min.size = 25, max.size = 500)

Arguments

geneSetList	A gene set collection stored in a list.
candidateGenes	A character vector of all genes to be considered.
min.size	Minimum number of genes to keep a gene set. Cannot be smaller than 2.
max.size	Maximum number of genes to keep a gene set.

Value

Filtered list of gene sets. This output can be used to construct gene set edge groups with the 'getGeneSetEdgeGroup' function.

Examples

## NOT RUN
# filterGeneSets(gscv7.0$kegg, colnames(ahba), min.size = 5, max.size = Inf)

Mengbo-Li/brainClass documentation built on March 16, 2023, 12:06 p.m.