simulatedData: GSEMA synthetic data

In GSEMA: Gene Set Enrichment Meta-Analysis

GSEMA synthetic data

Description

• study1Ex, study2Ex: two expression matrices.

• study1Pheno, study2Pheno: two phenodata objects.

• GeneSets: a list of gene sets with each element are the genes that belong to a pathway.

• objectMApathSim: the meta-analysis object created from the different expression matrices and phenodatas.

Usage

data(simulatedData)

Format

arrays (study1Ex, study2Ex), data.frames (study1Pheno, study2Pheno), list vectors (GeneSets) and list of nested lists (objectMApathSim).

Source

study1Ex, study2Ex, study1Pheno and study2Pheno are synthetic. GeneSets was created from the information of MsigDB database by adding a simulated pathway with simulated genes

objectMApathSim was created after using createObjectMA GSEMA function to the different studies objects and with the information of GeneSets object

maObjectDif was created after using createObjectMA DExMA function to the listExpressionSets object. maObject was obtained after using allSameID function to maObjectDif function.

References

Liberzon A, Birger C, Thorvaldsdóttir H, Ghandi M, Mesirov JP, Tamayo P. The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Syst. 2015;1: 417–425

GSEMA documentation built on Oct. 14, 2024, 5:09 p.m.