gmtEnsembl: gmtEnsembl

In Krutik6/TimiRGeN: Time sensitive microRNA-mRNA integration, analysis and network generation tool

gmtEnsembl

Description

Change entrez IDs in path_gene and path_data into ensembl IDs. Will create two new dataframes with ensembl IDs and wikipathway information.

Usage

gmtEnsembl(MAE, path_gene, path_data, orgDB)

Arguments

MAE	MultiAssayExperiment which will store the output of gmtEnsembl. It is recommended to use the same MAE object which contains output from dloadGmt.
path_gene	Dataframe with wikipathway IDs and entrezgene IDs. path_gene is from the dloadGmt function. It will be stored as an assay within the MAE used in the dloadGmt function.
path_data	Dataframe with wikipathway IDs, wikipathway names and entrezgene IDs. path_data is from the dloadGmt function. It will be stored as an assay within the MAE used in the dloadGmt function.
orgDB	Load the appropriate db package e.g. org.Hs.eg.db if human wikipathways are being used.

Value

2 dataframes. One containing wikipathway IDs and ensembl gene IDs, and the other containing wikipathway IDs, ensembl gene IDs and wikipathway names. Output will be stored as assays in the input MAE.

Examples

library(org.Mm.eg.db)

miR <- mm_miR[1:50,]

mRNA <- mm_mRNA[1:100,]

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

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

MAE <- gmtEnsembl(MAE = MAE, assay(MAE, 3),
                   assay(MAE, 5), org.Mm.eg.db)

Krutik6/TimiRGeN documentation built on Jan. 27, 2024, 7:46 p.m.