LEANR: Finds "Local Subnetworks" Within an Interaction Network which Show Enrichment for Differentially Expressed Genes

Implements the method described in "Network-based analysis of omics data: The LEAN method" [Gwinner Boulday (2016) <DOI:10.1093/bioinformatics/btw676>] Given a protein interaction network and a list of p-values describing a measure of interest (as e.g. differential gene expression) this method computes an enrichment p-value for the protein neighborhood of each gene and compares it to a background distribution of randomly drawn p-values. The resulting scores are corrected for multiple testing and significant hits are returned in tabular format.

Install the latest version of this package by entering the following in R:
install.packages("LEANR")
AuthorFrederik Gwinner
Date of publication2016-11-12 15:47:01
MaintainerFrederik Gwinner <frederik.gwinner@gmail.com>
LicenseGPL-3
Version1.4.9

View on CRAN

Files

inst
inst/extdata
inst/extdata/g_red.sif.gz
inst/extdata/gene.annots.txt.gz
inst/extdata/input_pvals_CCM2.txt.gz
inst/extdata/pvals_red.txt.gz
inst/extdata/STRING_Mouse_fs900.sif.gz
inst/doc
inst/doc/CCM-data.html
inst/doc/subnet-sim.Rmd
inst/doc/subnet-sim.R inst/doc/CCM-data.R
inst/doc/CCM-data.Rmd
inst/doc/subnet-sim.html
tests
tests/testthat.R
tests/testthat
tests/testthat/test_output.R tests/testthat/test_graphmod.params.R
NAMESPACE
data
data/gene.annots.rda
data/g_red.rda
data/gene.list.scores.rda
data/datalist
data/CCM.pvals.rda
data/pvals_red.rda
data/g2.rda
R
R/sysdata.rda
R/leanr_method.R
vignettes
vignettes/subnet-sim.Rmd
vignettes/CCM-data.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/g2.Rd man/LEANR-package.Rd man/subnet.simulation.Rd man/run.lean.Rd man/CCM.pvals.Rd man/gene.list.scores.Rd man/gene.annots.Rd man/get.ls.info.Rd man/pvals_red.Rd man/g_red.Rd man/write.ls.to.sif.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.