get_path_names: Tranlates path IDs to path names

In babelomics/hipathia: HiPathia: High-throughput Pathway Analysis

Tranlates path IDs to path names

Description

Translates the subpathway IDs to readable and comprensible names.

For effector subpathways, the names of the subpathways are encoded as "pathway: effector_protein", where "pathway" is the pathway to which the subpathway belongs and "effector_protein" is the name of the last node in the subpathway.

For decomposed subpathways, the names of the subpathways are encoded as "pathway: receptor_protein - effector_protein", where "pathway" is the pathway to which the subpathway belongs, "receptor_protein" is the name of the initial node of the subpathway and "effector_protein" is the name of the last node in the subpathway.

Usage

get_path_names(metaginfo, names, maxchar = NULL)

Arguments

metaginfo	Pathways object
names	Character vector with the subpathway IDs to be translated
maxchar	Integer, describes the number of maximum characters to be shown. By default no filter is applied.

Value

A character vector including the readable names of the subpathways IDs, in the same order as provided.

Examples

data(path_vals)
pathways <- load_pathways(species = "hsa", pathways_list = c("hsa03320",
"hsa04012"))
translated_names <- get_path_names(pathways, rownames(path_vals))

babelomics/hipathia documentation built on July 27, 2022, 2:23 p.m.