turnPercent {TimiRGeN} | R Documentation

## turnPercent

### 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))

[Package TimiRGeN version 1.0.6 Index]