combineGenes {TimiRGeN} | R Documentation

## 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))

[Package TimiRGeN version 1.2.0 Index]