wikiMatrix: wikiMatrix

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

Description

Creates a matrix which shows how many genes from the input mRNA and miRNA data are found in each wikipathway, for a specific species.

Usage

wikiMatrix(MAE, ID_list, wp_list)

Arguments

MAE	MultiAssayExperiment which will store the output of wikiMatrix. It is recommended that the MAE object which stores output from the wikiList function.
ID_list	List of lists of entrez gene IDs or ensembl gene IDs stored as strings. This is the output of the eNames function and is stored as metadata in the MAE used in the eNames function.
wp_list	List of lists containing wikipathways with entrez gene IDs or ensembl IDs as strings. This is the output of the wikiList function and is stored as metadata in the MAE used in the wikiList function.

Value

A matrix showing which genes are found in each time points for each pathway. Output will be stored as an assay in the input MAE.

Examples

MAE <- MultiAssayExperiment()

metadata(MAE)[["ID_list"]] <- e_list_mouse

metadata(MAE)[["w_list"]] <- w_list_mouse[1:10]

MAE <- wikiMatrix(MAE, ID_list = metadata(MAE)[[1]],
                  wp_list = metadata(MAE)[[2]])

TimiRGeN documentation built on April 17, 2021, 6:03 p.m.