getClusterManyParams: Get parameter values of clusterMany clusters

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

Get parameter values of clusterMany clusters

Description

Takes an input a ClusterExperiment object and returns the parameter values used in creating the clusters that were created by 'clusterMany'

Usage

## S4 method for signature 'ClusterExperiment'
getClusterManyParams(
  x,
  whichClusters = "clusterMany",
  searchAll = FALSE,
  simplify = TRUE
)

Arguments

x	a ClusterExperiment object that contains clusterings from running clusterMany.
whichClusters	argument that can be either numeric or character vector indicating the clusterings to be used. See details of getClusterIndex.
searchAll	logical, indicating whether all clusterings with clusterMany label should be allowed (i.e. including those from previous ones with labels like clusterMany.1), or only limited to those in most recent workflow (default).
simplify	logical. Whether to simplify the output so as to remove features that do not change across the clusterings.

Details

The method simply parses the clusterLabels of the indicated clusterings, relying on the specific format used by clusterMany to create labels. The function will only allow the parsing to be performed on those clusterings with a 'clusterMany' clusterType. If the user has manipulated the clusterLabels manually or manually identified the clusterType of a clustering as 'clusterMany', this function may create unexpected results or errors. Similarly, it cannot be used on 'clusterMany' results from an old iteration (e.g. that have type 'clusterMany.1')

Specifically, it splits the label of each clustering by the character ",", as indicating the different parameters; this should return a value of form "ABC=123". The function then pulls out the numeric value ('123') and associates that value as the value of the parameter ('ABC')

Value

Returns a data.frame where the column names are the parameter names, and the entries are the values of the parameter for the indicated clustering. The column 'clusteringIndex' identifies the index of the clustering in the full set of clusterings of the given ClusterExperiment object.

Examples

## Not run: 
data(simData)

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

## End(Not run)

epurdom/clusterExperiment documentation built on April 28, 2024, 8:17 p.m.