DrugCombination: Treatment Efficacy of the Drug Combination.

In lanagarmire/Asgard: A Single-cell Guided pipeline for Accurate Repurposing of Drugs

Treatment Efficacy of the Drug Combination.

Description

It evaluates treatment efficacy to identify drug combinations that can best reverse the target genes’ expression in diseased cells in case samples.

Usage

DrugCombination(
  SC.integrated = SC.data,
  Gene.data = Gene.list,
  Drug.data = Drug.ident.res,
  Drug.FDR = 0.1,
  FDA.drug.only = TRUE,
  Combined.drugs = 2,
  GSE92742.gctx = NULL,
  GSE70138.gctx = NULL,
  Case = NULL,
  Tissue = "breast"
)

Arguments

SC.integrated	A Seurat object of aligned single cells from SCalignment function.
Gene.data	A list of differnential gene expression profiles for every cell type. It's from GetGene function.
Drug.data	A list of mono-drugs for every cell type. It's from GetDrug function.
Drug.FDR	The FDR threshold to select drug. The default value is 0.1.
FDA.drug.only	logical; if TRUE, will only return FDA-approved drugs.
Combined.drugs	The number of drugs in a combination. The default value is 2.
GSE92742.gctx	The gctx file contains drug responses from GSE92742 dataset (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92742).
GSE70138.gctx	The gctx file contains drug responses from GSE70138 dataset (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70138).
Case	A vector contains names of case samples.
Tissue	Reference tissue. If one used lung_rankMatrix.txt in GetDrugRef function, then the Reference tissue is lung.

Details

This function evaluates treatment efficacy and ranks drug combinations using therapeutics score, which integrates gene responses to multiple drugs, the proportion of genes, and cells treated by combined drugs.

Value

A data frame of drug combinations with therapeutics scores and FDR.

lanagarmire/Asgard documentation built on Jan. 25, 2024, 3:28 p.m.