wikiMrna {TimiRGeN} | R Documentation

## wikiMrna

### Description

Identify genes that are in common in both the wikipathway of interest and the significantly differentially expressed input mRNAs.

### Usage

    wikiMrna(MAE, mRNA_express, singleWiki, stringWiki='')

### Arguments

`MAE` | MultiAssayExperiment which will store the results of wikiMrna. It is recommended to use the same MAE which stores output from the diffExpressRes and reduceWiki functions.
`mRNA_express` | Dataframe from the diffExpressRes function used on the input mRNA data. This should be found as an assay within the MAE used in the diffExpressRes function.
`singleWiki` | Dataframe containing information about only one pathway. This is output from the reduceWiki function. This should be found as an assay within the MAE used in the reduceWiki function.
`stringWiki` | Name of the pathway of interest. Should be the same as the stringWiki parameter from the reduceWiki function.

### Value

A dataframe which only contains mRNAs which are found in both the input data and the wikipathway of interest. Output will be stored as an assay in the input MAE.

### Examples

    library(org.Mm.eg.db)

    miR <- mm_miR[1:200,]

    mRNA <- mm_mRNA[401:600,]

    MAE <- startObject(miR = miR, mRNA = mRNA)

    MAE <- getIdsMir(MAE, assay(MAE, 1), orgDB = org.Mm.eg.db, 'mmu')

    MAE <- getIdsMrna(MAE, assay(MAE, 2), "useast", 'mmusculus')

    MAE <- dloadGmt(MAE = MAE, species = "Mus musculus")

    MAE <- reduceWiki(MAE, path_data = assay(MAE, 11),
                      stringWiki = 'TGF Beta Signaling Pathway')

    MAE <- diffExpressRes(MAE, df = assay(MAE, 2), dataType = 'Log2FC',
                   genes_ID = assay(MAE, 7),
                   idColumn = 'GENENAME',
                   name = "mRNA_log")

    MAE <- wikiMrna(MAE, mRNA_express = assay(MAE, 13),
                    singleWiki = assay(MAE, 12),
                    stringWiki = 'TGF Beta Signaling Pathway')

[Package TimiRGeN version 1.2.0 Index]