genesets_sel: Selected gene sets as test

In oriolarques/GSEAmining: Make Biological Sense of Gene Set Enrichment Analysis Outputs

Selected gene sets as test

Description

Data that corresponds to GSEA analysis of differential expressed genes from treated versus control samples in HGPalmer-PDX-P30 experiment. Differential gene expression was obtained by using the oligo and limma R packages. GSEA analysis was performed using the clusterProfiler R package using MSigDb collections C2, C5 and Hallmarks.

Usage

data(genesets_sel)

Format

An object of class data.frame with 52 observations and 4 variables:

ID

Name of the gene set

NES

Normalized Enrichment Score

p.adjust

False discovery rate

core_enrichment

Genes that are in the leading edge subset

Source

ArrayExpress

References

Arqués et al. Clinical Cancer Research. 2016 Feb 1;22(3):644-56. doi: 10.1158/1078-0432.CCR-14-3081. Epub 2015 Jul 29. (Clinical Cancer Research)

Examples

data(genesets_sel)

gs.cl <- gm_clust(genesets_sel)

gm_dendplot(genesets_sel, gs.cl)

gm_enrichterms(genesets_sel, gs.cl)

gm_enrichcores(genesets_sel, gs.cl)

## Not run: gm_enrichreport(genesets_sel, gs.cl)

oriolarques/GSEAmining documentation built on June 27, 2023, 11:31 p.m.