turnPercent: turnPercent

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

Description

Genes found in common between the input data and each pathway are normalised by percentages. This is to normalise for pathway size.

Usage

turnPercent(MAE, wikiMatrix)

Arguments

MAE	MultiAssayExperiment which will store the output from turnPercent. It is recommended to use the MAE which stores output from the wikiMatrix function.
wikiMatrix	Numeric matrix of wikipathways and samples. This should be stored as an assay within the MAE used in the wikiMatrix function.

Value

A percentage matrix which contrasts genes found in pathways and samples. Output will be stored as an assay within the input MAE.

Examples

MAE <- MultiAssayExperiment()

metadata(MAE)[["e_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]])

MAE <- turnPercent(MAE = MAE, wikiMatrix = assay(MAE, 1))

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