workflowClusters: Methods for workflow clusters

In epurdom/clusterCells: Compare Clusterings for Single-Cell Sequencing

Methods for workflow clusters

Description

The main workflow of the package is made of clusterMany, makeConsensus, and mergeClusters. The clusterings from these functions (and not those obtained in a different way) can be obtained with the functions documented here.

Usage

## S4 method for signature 'ClusterExperiment'
workflowClusters(x, iteration = 0)

## S4 method for signature 'ClusterExperiment'
workflowClusterDetails(x)

## S4 method for signature 'ClusterExperiment'
workflowClusterTable(x)

## S4 method for signature 'ClusterExperiment'
setToCurrent(x, whichCluster, eraseOld = FALSE)

## S4 method for signature 'ClusterExperiment'
setToFinal(x, whichCluster, clusterLabel)

Arguments

x	a ClusterExperiment object.
iteration	numeric. Which iteration of the workflow should be used.
whichCluster	argument that can be a single numeric or character value indicating the single clustering to be used. Giving values that result in more than one clustering will result in an error. See details of getClusterIndex.
eraseOld	logical. Only relevant if input x is of class ClusterExperiment. If TRUE, will erase existing workflow results (clusterMany as well as mergeClusters and makeConsensus). If FALSE, existing workflow results will have "_i" added to the clusterTypes value, where i is one more than the largest such existing workflow clusterTypes.
clusterLabel	optional string value to give to cluster set to be "final"

Value

workflowClusters returns a matrix consisting of the appropriate columns of the clusterMatrix slot.

workflowClusterDetails returns a data.frame with some details on the clusterings, such as the type (e.g., 'clusterMany', 'makeConsensus') and iteration.

workflowClusterTable returns a table of how many of the clusterings belong to each of the following possible values: 'final', 'mergeClusters', 'makeConsensus' and 'clusterMany'.

setToCurrent returns a ClusterExperiment object where the indicated cluster of whichCluster has been set to the most current iteration in the workflow. Pre-existing clusters are appropriately updated.

setToFinal returns a ClusterExperiment object where the indicated cluster of whichCluster has clusterType set to "final". The primaryClusterIndex is also set to this cluster, and the clusterLabel, if given.

Examples

## Not run: 
data(simData)

cl <- clusterMany(simData,nReducedDims=c(5,10,50),  reduceMethod="PCA",
clusterFunction="pam", ks=2:4, findBestK=c(FALSE), removeSil=TRUE,
subsample=FALSE, makeMissingDiss=TRUE)

clCommon <- makeConsensus(cl, whichClusters="workflow", proportion=0.7,
minSize=10)

clCommon <- makeDendrogram(clCommon)

clMerged <- mergeClusters(clCommon,mergeMethod="adjP", DEMethod="limma")

head(workflowClusters(clMerged))
workflowClusterDetails(clMerged)
workflowClusterTable(clMerged)

## End(Not run)

epurdom/clusterCells documentation built on April 23, 2024, 9:06 p.m.