combineGenes: combineGenes

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

combineGenes

Description

Combines miR and mRNA data into one dataframe. Input columns should be written as : timepoint.DifferentialExpressionResultType e.g. D1.log2fc or H6.adjPval. Column names should be the same for miR and mRNA data. If a more detailed explanation of column nomenclature is needed please read the vignette. combineGenes is essential for combined analysis of miR-mRNA data. If using separate analysis, there is no need to use combineGenes.

Usage

combineGenes(MAE, miR_data, mRNA_data)

Arguments

MAE	Input MAE which stores results from combineGenes. It is recommended to use the MAE which was used in startObject.
miR_data	microRNA dataframe. Rows should be genes, columns are DE results and time point. This should be the stored as an assay within the MAE used in the startObject function.
mRNA_data	mRNA dataframe. Rows should be genes, columns are DE results and time point. This should be the stored as an assay within the MAE used in the startObject function.

Value

A dataframe with combined miR and mRNA data. Will be stored as an assay in the input MAE.

Examples

library(org.Mm.eg.db)

data(mm_miR)

data(mm_mRNA)

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

MAE <- combineGenes(MAE = MAE, miR_data = assay(MAE, 1),
                    mRNA_data = assay(MAE, 2))

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