clusterCheck: clusterCheck

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

clusterCheck

Description

clusterCheck creates a PCA plot using functions from Mfuzz. This will help to indicate if an appropriate number of clusters have been created. The closer the circles are to one another the more likely that they should belong to the same cluster. Read more about Mfuzz here https://bioconductor.org/packages/release/bioc/html/rWikiPathways.html.

Usage

clusterCheck(Clusters, W)

Arguments

Clusters	A large list of clusters, statistics and phenodata. This will be stored as metadata within the MAE used in the createClusters function.
W	TRUE or FALSE. Should the plot be shown in a new window? Default is FALSE.

Value

A PCAplot showing distance of clusters.

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)

clusterCheck(Clusters = metadata(MAE)[[3]], W = FALSE)

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