dataMiningMatrix: dataMiningMatrix

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

Description

Mines out predicted/ functional interactions which correspond between miR-mRNA interactions found in Targetscans, miRDB, miRTarBase and the interactions from the miR-mRNA correlation matrix. If a database cannot be downloaded, dataMiningMatrix can be used regardless, but it is recommended to download all three databases.

Usage

dataMiningMatrix(MAE, corrTable, targetscan , mirdb, mirtarbase)

Arguments

MAE	MultiAssayExperiment which will store the output of dataMiningMatrix. It is recommended to use the MAE object which stores output from the mirMrnaInt function.
corrTable	Correlation matrix of interactions between the mRNAs from a pathway of interest and miRNA data. This is created by the mirMrnaInt function and should be stored as an assay within the MAE used in the mirMrnaInt function.
targetscan	Species specific miR-mRNA interactions predicted by targetscans. This is the output from the dloadTargetscan function. It should be stored as an assay within the MAE used in the dloadTargetscan function. If this data cannot be downloaded, dataMiningMatrix can be run without it.
mirdb	Species specific miR-mRNA interactions predicted by miRDB. This is the output from the dloadMirdb function. It should stored as an assay within the MAE used in the dloadMirdb function. If this data cannot be downloaded, dataMiningMatrix can be run without it.
mirtarbase	Species specific miR-mRNA interactions which are functionally curated by mirtarbase. This is the output from the dloadMirtarbase function. It should be stored as an assay within the MAE used in the dloadMirtarbase function. If this data cannot be downloaded, dataMiningMatrix can be run without it.

Value

A matrix which cross references the occurrences of miR-mRNA interactions between databases and the given data. Output will be stored as an assay in the input MAE.

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