prune: Pruning of a gene list by interaction distance to seed genes

In kkmann/pwcuratr: Functional Pathway Cluster Curation tool

Description

Prune a list of genes by maximal edge distance from provided seed genes using gene-gene functional interactions as edges.

Usage

prune(genes, seed_genes, minscore = 0, maxedgedistance = Inf)

Arguments

genes	character vector of ensembl IDs
seed_genes	character vector of ensembl IDs
minscore	minimal evidence score for edges to include (see as_igraph())
maxedgedistance	only genes that are connected to any of the seed genes via maxedgedistance or less edges (interactions) are retained

Value

a character vector with retained genes, always containes all seed genes

Examples

prune(c("ENSG00000130203", "ENSG00000189058"), c("ENSG00000130203"), 0.9, 2)

kkmann/pwcuratr documentation built on March 7, 2020, 2 a.m.