clusterList: clusterList

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

Description

clusterList will transform clusters created by createClusters2 into lists based on which genes associate most to each cluster. Genes which associate with a cluster are determined by the fitCluster parameter in the function.

Usage

clusterList(MAE, clusterData, fitCluster, miR_IDs, mRNA_IDs)

Arguments

MAE	MultiAssayExperiment which will store the results from createClusters.
clusterData	A dataframe which contains cluster-pathway fit scores and is stored as an assay within the MAE used in the createClusters2 function.
fitCluster	Integer from 0-1. How well should genes fit into a cluster? Default is 0.5.
miR_IDs	miR_ensembl or miR_entrez. Use a getIDsMir function to acquire this. This will be stored as an assay in the MAE used in a getIdsMir function.
mRNA_IDs	mRNA_ensembl or mRNA_entrez. Use a getIDsMrna function to acquire this. This will be stored as an assay in the MAE used in a getIdsMrna function.

Value

A list containing the genes which fit to each cluster.

Examples

library(org.Hs.eg.db)

data(long_data)

miRNA <- long_data[c(1:105),]

mRNA <- long_data[-c(1:105),]

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

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

MAE <- getIdsMrna(MAE, assay(MAE, 2), mirror = 'useast', 'hsapiens')

MAE <- combineGenes(MAE, miR_data = assay(MAE, 1),
                    mRNA_data = assay(MAE, 2))

MAE <- createClusters2(MAE = MAE, genetic_data = assay(MAE, 9),
                       noClusters =2)

MAE <- clusterList(MAE = MAE, clusterData = assay(MAE, 11), fitCluster = 0.5,
                   miR_IDs = assay(MAE, 3),
                   mRNA_IDs = assay(MAE, 7))

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