DrugScore: Calculate drug score

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

Calculate drug score

Description

The drug score is a comprehensive estimation of drug therapeutic effects using all or a selected set of clusters.

Usage

DrugScore(
  cell_metadata,
  cluster_degs,
  cluster_drugs,
  tissue,
  gse70138_gctx_path,
  gse92742_gctx_path,
  clusters = NULL,
  case = NULL,
  fda_drugs_only = TRUE
)

Arguments

cell_metadata	A data.frame of cell metadata. It must have a column named 'cluster' indicating which cluster cells belong, and a column named 'sample' indicating which sample cells belong.
cluster_degs	A list of differential gene expression profiles for each cluster.
cluster_drugs	Drug repurposing result from GetDrug function.
tissue	Reference tissue. If one used 'lung_rankMatrix.txt' in GetDrugRef function, then the Reference tissue is lung. Please use " " instead of "-" in tissue name. For example, while 'haematopoietic-and-lymphoid-tissue' is the prefix of the drug reference files, the corresponding tissue name is "haematopoietic and lymphoid tissue".
gse70138_gctx_path	The gctx file contains drug responses from GSE70138 dataset (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70138).
gse92742_gctx_path	The gctx file contains drug responses from GSE92742 dataset (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92742)..
clusters	Select which clusters (cell types) to be used for drug score estimation. By default, it uses all clusters.
case	A vector containing case sample names.
fda_drugs_only	logical; if TRUE, will only return FDA-approved drugs, else, will return all drugs/compounds.

Details

This function calculates drug score using cellular proportion of clusters, the significance of reversal in DEGs' expressions, and the ratio of the reversed genes.

Value

A data frame of drug score, P-value and FDR.

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