combineGenes: combineGenes

Description Usage Arguments Value Examples

View source: R/combineGenes.R

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

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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

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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))

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