SPACEconnect: SPACEconnect: is a new method to visualise correlations...

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

SPACEconnect: is a new method to visualise correlations between experimental gene expression profiles and drug connectivity map profiles

Description

The SPACEconnect package provides three categories of important functions: computePeturbEnrichment, computeComboEnrichment and plotDrugConnectivity.

SPACEconnect functions

computeComboEnrichment: Compute drugs Enrichment of combination of two drugs. USAGE computeComboEnrichment(mFC, mDrugEnrich, DrugsAnnot, ntop = 10, nsample = 20, nprune = 250, contrast = NULL, res.mono = NULL)

computePeturbEnrichment: Compute drug Enrichment, drugs activity or drugs sensitivity based on database and annotation provided as input parameter USAGE: computePeturbEnrichment(mFC = mFC, mDrugEnrich = mDrugEnrich, DrugsAnnot = DrugsAnnot,methods = "GSEA", nprune = 250, contrast = NULL)

dseaPlotActmap: Plot drug Activity Map. USAGE: dseaPlotActmap(dsea, drugs, method = "GSEA", contr, nterms = 50, nfc = 20)

getActiveDSEA: Create the drug set enrichment object that is used in the visualization USAGE: getActiveDSEA(mDrugEnrich, DrugsAnnot, mFC, contr = NULL)

getMOA: Get the mechanism of action object USAGE: getMOA(dsea)

plotDrugConnectivity: Plot Drug Connectivity USAGE: plotDrugConnectivity(dsea)

plotMOA: Plot mechanism of action USAGE: plotMOA(dsea, ntop = 16)

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