gene.list.scores


  Gene p-value list used in examples for function run.lean.fromdata
  Contains p-values obtained from a limma differential expression analysis


datasets

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.

Frederik Gwinner

LEANR

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

gene.list.scores function

The format is:
 Named num [1:7342] 0.772 0.813 0.979 0.841 0.607 ...
 - attr(*, "names")= chr [1:7342] "10090.ENSMUSP00000000001" "10090.ENSMUSP00000010205" "10090.ENSMUSP00000053818" "10090.ENSMUSP00000000153" ...

gene.list.scores: Gene p-value list used in examples for function run.lean.fromdata

Description

Usage

Arguments

Format