reduceWiki: reduceWiki

In Krutik6/TimiRGeN: Time sensitive microRNA-mRNA integration, analysis and network generation tool

reduceWiki

Description

Returns all gene IDs of a single wikipathway of interest. This function is recommended to be used after a signalling pathway of interest is found.

Usage

reduceWiki(MAE, path_data, stringWiki = '')

Arguments

MAE	MultiAssayExperiment which will store the results of reduceWiki. It is recommended to use the same MAE which stores the data from dloadGmt/ gmtEnsembl.
path_data	Dataframe with wikipathway IDs, gene IDs and pathway names from either the dloadGmt or gmtEnsembl functions. These will be found as assays within the MAE used in the dloadGmt or gmtEnsembl functions.
stringWiki	Full name of the wikipathway of interest. Make sure to spell this correctly. Each wikipathway can only be added once to the same MAE object.

Value

A dataframe that only contains information about the wikipathway of interest. Output will be stored as an assay in the input MAE.

Examples

MAE <- MultiAssayExperiment(list(path_data = data.frame(
                        "wpid" = c(rep("WP571", 6)),
                        "gene" = c(16175, 12370,26419, 19249, 19645, 18479),
                        "name" = c(rep("Fas pathway and Stress induction of HSP regulation",
                        6)))))

MAE <- reduceWiki(MAE, path_data = assay(MAE, 1),
                 stringWiki = 'Fas pathway and Stress induction of HSP regulation')

Krutik6/TimiRGeN documentation built on Jan. 27, 2024, 7:46 p.m.