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.

Author
Frederik Gwinner
Date of publication
2016-11-12 15:47:01
Maintainer
Frederik Gwinner <frederik.gwinner@gmail.com>
License
GPL-3
Version
1.4.9

View on CRAN

Man pages

CCM.pvals
Gene p-value list derived from knock-out experiments of the...
g2
igraph graph object used in examples for function...
gene.annots
Annotation for STRING protein Ids
gene.list.scores
Gene p-value list used in examples for function...
get.ls.info
Extract the genes of a "local subnetwork"" around a given...
g_red
igraph graph object used in unit tests
LEANR-package
Finds "local subnetworks" within an interaction network which...
pvals_red
Gene p-value list used in unit tests
run.lean
Run the LEAN approach
subnet.simulation
Simulate subnetworks
write.ls.to.sif
Extract the "local subnetwork" around a given protein

Files in this package

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