wikiMrna: wikiMrna

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

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')

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