computePeturbEnrichment: Compute drug Enrichment, drugs activity or drugs sensitivity...

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

Compute drug Enrichment, drugs activity or drugs sensitivity based on database and annotation provided as input parameter

Description

Compute drug Enrichment, drugs activity or drugs sensitivity based on database and annotation provided as input parameter

Usage

computePeturbEnrichment(
  mFC,
  mDrugEnrich,
  DrugsAnnot,
  methods = c("GSEA", "cor"),
  nmin = 15,
  nprune = 0,
  contrast = NULL
)

Arguments

mFC	= A matrix of differential gene expression fold-change of own experiment, the rows name of the matrix must be the genes names
mDrugEnrich	= a large matrix represents the gene expression fold change in the presence of different perturbations, either various drugs concentrations or other genetic engineering techniques as gene-knock-in etc..
DrugsAnnot	=is matrix represents the drugs annotation that contains the targets, mechanism of action , clinical phase, disease area, and indication
methods	the computation methods of Enrichment, either using GSEA algorithm or the rank correlation.
nmin	the minimum number of drugs
nprune	takes only the (nprune) top matching drugs for each comparison to reduce the size of the matrix. default is 0 to take the full matrix
contrast	is a character string represent the two compared conditions(contrast) as it is provided from the fold-change matrix

Value

drugs a list of drugs enrichment stats and annotations

Examples

# from the data-sets provided as examples within the package load the .rda files
# DrugsAnnot, mDrugEnrich, mFC
drugs <- computePeturbEnrichment(
  mFC = mFC, mDrugEnrich = mDrugEnrich, DrugsAnnot = DrugsAnnot,
  methods = "GSEA", nprune = 250, contrast = NULL
)

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