returnCluster {TimiRGeN} | R Documentation |
Retrieves information about which wikipathways fitted best to a specific cluster. This function is to be used after quickFuzz.
returnCluster(MAE, clusterData, whichCluster, fitCluster)
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. |
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.
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)