genesets_sel: Selected gene sets as test

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

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)

GSEAmining documentation built on Nov. 8, 2020, 5:52 p.m.