Pruning of a gene list by interaction distance to seed genes

Source: R/prune.R

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

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)
#> [1] "ENSG00000130203"