addPrefix: addPrefix

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

Description

Adds 'miR_' or 'mRNA_' genetypes to colnames of dataframes. Resulting colnames should be in the following naming system: 'genetype_timepoint.resulttype'. This function is essential for separate analysis of miR-mRNA DE data. If using the combined analysis, there is no need to use addPrefix.

Usage

addPrefix(MAE, gene_df, prefixString = '')

Arguments

MAE	MultiAssayExperiment to store output of addPrefix. It is recommended to use the MAE object which stores output from startObject.
gene_df	Dataframe of mRNA or miR results from differential expression analysis. Will be stored as an assay within the MAE used in the startObject function.
prefixString	Prefix to be added e.g. "miR" or "mRNA".

Value

Dataframe which has a specific prefix infront of each column name. Will be stored as an assay in the input MAE.

Examples

data(mm_miR)

data(mm_mRNA)

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

MAE <- addPrefix(MAE = MAE, gene_df = assay(MAE, 1),
                 prefixString = "miR")

MAE <- addPrefix(MAE = MAE, gene_df = assay(MAE, 2),
                 prefixString = "mRNA")

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