bcMigsaResAsList: A MIGSA results object obtained from breast cancer data.

In jcrodriguez1989/MIGSAdata: MIGSA vignette data

Description

A MIGSA results object obtained using the datasets:

• mainz (microarray).

• nki (microarray).

• tcga (microarray).

• tcga (RNAseq).

• transbig (microarray).

• unt (microarray).

• upp (microarray).

• vdx (microarray).

Format

A list with two main components to create the MIGSAres object

Details

Each dataset subjects were classified using the PAM50 algorithm. For this analysis only Basal and Luminal A subjects were kept (this was the contrast used, i.e., Basal vs. LumA).

Datasets were tested for gene set enrichment over:

• the org.Hs.eg.db Gene Ontology gene sets, resulting in 14,291 as BP, 1,692 CC and 4,263 MF.

• KEGG gene sets downloaded from enrichr database resulting in 179 gene sets.

In order to get the MIGSAres object follow: library(MIGSAdata); library(MIGSA); data(bcMigsaResAsList); bcMigsaRes <- MIGSA:::MIGSAres.data.table(bcMigsaResAsList$dframe, bcMigsaResAsList$genesRank);

jcrodriguez1989/MIGSAdata documentation built on May 18, 2019, 10:26 p.m.