startObject: startObject

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

startObject

Description

Creates a MultiAssayExperiment (MAE) from miR and mRNA dataframes. MAE's will be the constant object used throughout TimiRGeN. The input dataframes should contain rows as genes, and results from differential expression (DE) as columns. Columns should also indicate the time point related to each sample. Row names and column names must adhere to TimiRGeN friendly nomenclature. Please do read the vignette for a full description of the required nomenclature.

Usage

startObject(miR, mRNA)

Arguments

miR	microRNA dataframe/ matrix. Rows should be miR gene names which use the TimiRGeN friendly naming system. Columns should be results of DE and time points.
mRNA	mRNA dataframe/ matrix. Rows should be mRNA gene names. Columns should be results of DE and time points.

Value

MultiAssayExperiment containing miR and mRNA data stored as assays. Use assays(MAE, i) or MAE[[i]] to access assays. Use metadata(MAE)[[i]] to access metadata. Use experiments(MAE)[[i]] to access experiments.

Examples

data(mm_miR)

data(mm_mRNA)

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

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