getGeneSetEdgeGroup: Construct gene set edge groups for a gene set collection...

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

Construct gene set edge groups for a gene set collection (GSC) of interest

Description

The 'getGeneSetEdgeGroup' function generates the gene set edge groups in 'brainclass' classification.

Usage

getGeneSetEdgeGroup(geneExpr, geneSetList, cutoff = 0.99)

Arguments

geneExpr	The ROI-by-gene data frame or matrix. Potentially the output from the 'filterGeneExpr' function.
geneSetList	A gene set collection stored in a list. Potentially the output from the 'filterGeneSets' function
cutoff	The hard-thresholding cutoff on edge weights.

Value

A list object of vectors, each containing labels of edges that are the most highly weighted in the corresponding gene set expression network. Each item in the returned list represents a gene set edge group. These gene set edge groups are used as feature groups in 'brainclass' classification.

Examples

## NOT RUN
# data(ahba)
# data(gscv7.0)
# ahba <- filterGeneExpr(ahba)
# kegg <- filterGeneSets(geneSetList = gscv7.0$kegg,
# candidateGenes = colnames(ahba), min.size = 5, max.size = Inf)
# keggEdgeGrp <- getGeneSetEdgeGroup(geneExpr = ahba, geneSetList = kegg)

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