diffExpressRes: diffExpressRes

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

diffExpressRes

Description

diffExpressRes will produce a dataframe which contains data for only one result type, along with an ID of choice. It is recommended to use this function on a DE results which represents abundance such as log2fc or average expression, as this data will be averaged and correlated later in the analysis. This is to be used for miR and mRNA data individually.

Usage

diffExpressRes(MAE, df, dataType = '', genes_ID, idColumn = '',
name = '')

Arguments

MAE	MultiAssayExperiment to store the output of diffExpressRes within it. This function is to be used after pathways of interest have been identified by enrichWiki or returnCluster. It is recommended to store all diffExpressRes results in the MAE used in enrichWiki and/ or returnCluster.
df	mRNA or miR dataframe (rownames as genes and DE results as columns). These will be found as assays in the MAE object used within the startObject function.
dataType	Column name to take an average from e.g. "Log2FC", "AveExp". This string should be found consistently in the column names of your input data. It is recommended to use a DE result value which represents abundance, rather than confidence.
genes_ID	Dataframe that was created from a getIds function e.g. mRNA_ensembl or miR_entrez. Use the same ID type for miR and mRNA data. These dataframes will be found as assays within the MAE which stores results from the getIds functions.
idColumn	Name of column to use as the merge point. If Column names in getIds results have not been changed, it should be "GENENAME". Default has been left as "GENENAME".
name	New name of the assay. Should be a unique string. Remember each assay in a MAE must have a unique name.

Value

Dataframe with only a single result type from DE (e.g. Log2FC) and an ID type e.g. entrezIDs. Output will be stored as an assay in the input MAE.

Examples

library(org.Mm.eg.db)

miR <- mm_miR[1:50,]

mRNA <- mm_mRNA[1:100,]

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

MAE <- getIdsMir(MAE, assay(MAE, 1), orgDB = org.Mm.eg.db, 'mmu')

MAE <- getIdsMrna(MAE, assay(MAE, 2), "useast", 'mmusculus', orgDB = org.Mm.eg.db)

MAE <- diffExpressRes(MAE, df = assay(MAE, 2), dataType = 'Log2FC',
                     genes_ID = assay(MAE, 7),
                     idColumn = 'GENENAME',
                     name = "mRNA_log2fc")

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