get_dprimes: Extract unbiased effect sizes from meta-analysis by...

In ccmap: Combination Connectivity Mapping

Description

Function extracts mu (overall mean effect size) and dprimes (unbiased effect sizes from each contrast).

Usage

get_dprimes(es)

Arguments

es	Result of call to es_meta.

Details

Result used to query connectivity map drugs and predicted drug combinations.

Value

List containing:

meta	Named numeric vector with overall mean effect sizes for all genes from meta-analysis.
contrasts	List of named numeric vectors (one per contrast) with unbiased effect sizes for all measured genes.

See Also

es_meta.

Examples

library(crossmeta)
library(lydata)

data_dir <- system.file("extdata", package = "lydata")

# gather GSE names
gse_names  <- c("GSE9601", "GSE15069", "GSE50841", "GSE34817", "GSE29689")

# load previous differential expression analysis
anals <- load_diff(gse_names, data_dir)

# run meta-analysis
es <- es_meta(anals)

#get dprimes
dprimes <- get_dprimes(es)

ccmap documentation built on Nov. 8, 2020, 5:14 p.m.