getActiveDSEA: Create the drug set enrichment object that is used in the...

In bigomics/SPACEconnect: Stratified Perturbation Analysis by Correlation Enrichment of connectivity

Create the drug set enrichment object that is used in the visualization

Description

Create the drug set enrichment object that is used in the visualization

Usage

getActiveDSEA(mDrugEnrich, DrugsAnnot, mFC, contr = NULL)

Arguments

mDrugEnrich	a large matrix represents the gene expression fold change in the presence of different perturbations, either various drugs concentrations or other genetic engineering
DrugsAnnot	is matrix represents the drugs annotation that contains the targets, mechanism of action , clinical phase, disease area, and indication
mFC	A matrix of differential gene expression fold-change of own experiment, the rows name of the matrix must be the genes names
contr	is a character string represent the two compared conditions(contrast) as it is provided from the fold-change matrix

Value

drug set enrichment object

Examples

# from the data-sets provided as examples within the package load the .rda files
# DrugsAnnot, mDrugEnrich, mFC
dsea <- getActiveDSEA(mDrugEnrich, DrugsAnnot, mFC, contr = colnames(mFC)[1])

bigomics/SPACEconnect documentation built on March 19, 2022, 3:39 a.m.