README.md

In ks4471/cmapr: What the Package Does (One Line, Title Case)

Enrichment test for gene sets associated with a trait of interest for drugs profiled by Connectivity Map (CMAP) that act to reverse observed transcriptional changes

To run enrichment, install addR - contains all relevant functions, including dependencies for cmapr()

devtools::install_github("ks4471/addR")
library(adds)

gene set of interest split into up or down regulated in the phenotype of interest, if unknown, set all as up or down

input_gene_set=list(up=c("ABCA4","ABCG4","ACOT7","ACSM4"),down=c("AASDHPPT","ABCE1","ABHD13","ABRAXAS2"))

background - include all genes with a detectable signal in the experiment

all_genes_profiled=c("ABCA4","ABCG4","ACOT7","ACSM4","AASDHPPT","ABCE1","ABHD13","ABRAXAS2","AARS","AARS2","ABCE1","ABCF1")

test requires re-analysed data available at https://www.dropbox.com/s/18l1w2jbqld2mej/cmap.enrich.data.Rdata?dl=0

Load('cmap.enrich.data.Rdata')
cnet=cmapr(modg=input_gene_set,bkg=all_genes_profiled)
write.file(cnet$pval,file='out/cmap_enrichment_results.txt')

raw connectivity map CMAP data re-analysed with correction for batch and covariates

https://www.broadinstitute.org/connectivity-map-cmap

ks4471/cmapr documentation built on May 18, 2019, 3:38 a.m.