R/SPACEconnect.R

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
#'
#' The SPACEconnect package provides three categories of important functions:
#' computePeturbEnrichment, computeComboEnrichment and plotDrugConnectivity.
#'
#' @section 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)
#'
#'
#' @docType package
#' @name SPACEconnect
NULL
#> NULL