metaLINCS: an R package for meta-level analysis of LINCS L1000 drug signatures using stratified connectivity mapping

MetaLINCS calculates and visualizes the correlation between your experimental gene expression profile with perturbations signatures from the LINCS L1000 drug connectivity map. Summarizing the analysis with these perturbation databases is difficult because they consist of more than a million of profiles, corresponding to different cell lines and varying treatment concentrations. MetaLINCS attempts to efficiently calculate and easily visualize the results by performing meta-level enrichment tests on the connectivity scores. In this way, mechanism-of-action or gene targets are easily evident from the analysis.

Installation

You can install the development version of metaLINCS from GitHub with:

# install.packages("remotes")
remotes::install_github("bigomics/metaLINCS")

Example

This is a basic example which shows you how to use metaLINCS:

library(metaLINCS)

## First we compute the connectivity enrichment    
res <- computeConnectivityEnrichment(mFC, nprune=0)
names(res)

## Now compute the MoA enrichment
moa <- computeMoaEnrichment(res) 
names(moa)

## Plot the drugs connectivity using plotDrugConnectivity()
plotDrugConnectivity(res, contr=1)

## Plot the mechanism of action using plotMOA()
plotMOA(moa, contr=1, type="drugClass", ntop=20)
plotMOA(moa, contr=1, type="targetGene", ntop=20)
    
## Plot the drugs activity map using plotActivationMap()
plotActivationMap(res, nterms = 60, nfc=20, rot=FALSE)