query_drugs: Get correlation between query and drug signatures.

In hms-dbmi/drugseqr: GUI to Explore Single-Cell and Bulk RNA-Seq from Fastq to Pathways and Perturbations

Get correlation between query and drug signatures.

Description

Determines the pearson correlation between the query and each drug signature.

Usage

query_drugs(query_genes, drug_es, ngenes = 200)

Arguments

query_genes	Named numeric vector of differential expression values for query genes. Names are HGNC symbols.
drug_es	A matrix of differential expression values for drugs.
ngenes	The number of top differentially-regulated (up and down) query genes to use.

Details

Drugs with the largest positive and negative pearson correlation are predicted to, respectively, mimic and reverse the query signature. Values range from +1 to -1.

Value

Named vector of pearson correlations between query and drug combination signatures.

Examples

# load CMAP02 data
cmap_es <- dseqr.data::load_data('cmap_es_ind.qs')

# use first cmap_es signature as query
dprimes <- cmap_es[1:100, 1]
names(dprimes) <- row.names(cmap_es)[1:100]

# get correlations between query and drug signatures
res <- dseqr:::query_drugs(dprimes, cmap_es)

hms-dbmi/drugseqr documentation built on Feb. 15, 2024, 10:38 p.m.