dot-sum_alts_in_pathway: Sum Alterations in a Pathway

In MSKCC-Epi-Bio/gnomeR: Wrangle and analyze IMPACT and TCGA mutation data

Sum Alterations in a Pathway

Description

Sum Alterations in a Pathway

Usage

.sum_alts_in_pathway(
  gene_binary,
  pathway_list_item,
  pathway_name,
  count_pathways_by
)

Arguments

gene_binary	a binary matrix (see gene_binary())
pathway_list_item	a named list of length 1 with pathway name as name and vector of genes as first and only item in list
pathway_name	name of pathway

Value

a dataframe of 1 column of 0/1s indicating pathway activated yes/no

Examples

gene_binary <- create_gene_binary(mutation = gnomeR::mutations, cna = gnomeR::cna,
fusion = gnomeR::sv)
x <- .sum_alts_in_pathway(gene_binary,
 pathway_list_item = gnomeR::pathways[1],
  pathway_name = names(gnomeR::pathways[1]),
    count_pathways_by = "alteration")

MSKCC-Epi-Bio/gnomeR documentation built on Oct. 17, 2024, 3:39 p.m.