returnCluster: returnCluster

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

returnCluster

Description

Retrieves information about which wikipathways fitted best to a specific cluster. This function is to be used after quickFuzz.

Usage

returnCluster(MAE, clusterData, whichCluster, fitCluster)

Arguments

MAE	MultiAssayExperiment which will store the output from returnCluster. It is recommended to use the same MAE which stores output from the createClusters function.
clusterData	A dataframe which contains cluster-pathway fit scores and is stored as an assay within the MAE used in the createClusters function.
whichCluster	Integer which should corresponds to the cluster of interest.
fitCluster	Integer from 0-1. How well should the pathways fit into the selected cluster? Default is 0.99.

Value

A dataframe that contains information about the pathways that corresponded best with the chosen cluster. Output will be stored as an assay in the input MAE.

Examples

MAE <- MultiAssayExperiment()

metadata(MAE)[["e_list"]] <- e_list_mouse

metadata(MAE)[["w_list"]] <- w_list_mouse[1:10]

MAE <- wikiMatrix(MAE, ID_list = metadata(MAE)[[1]],
                  wp_list = metadata(MAE)[[2]])

MAE <- turnPercent(MAE = MAE,
                   wikiMatrix = assay(MAE, 1))

MAE <- createClusters(MAE, method = "c",
                    percentMatrix = assay(MAE, 2),
                    noClusters = 2, variance = 0.99)

MAE <- returnCluster(MAE, clusterData = assay(MAE, 3), whichCluster = 1,
                     fitCluster = 0.5)

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