calculateClustersSimilarity-scRNAseq: calculateClustersSimilarity

In ilyessr/conclus: ScRNA-seq Workflow CONCLUS - From CONsensus CLUSters To A Meaningful CONCLUSion

calculateClustersSimilarity

Description

Having computed cells similarity, pools information into clusters.

Usage

calculateClustersSimilarity(theObject, clusteringMethod = "ward.D2")

Arguments

theObject	An Object of class scRNASeq for which the count matrix was normalized (see ?normaliseCountMatrix), tSNE were calculated (see ?generateTSNECoordinates), dbScan was run (see ?runDBSCAN), and cells were clustered (see ?clusterCellsInternal).
clusteringMethod	Clustering method passed to hclust() function. See ?hclust for a list of method. Default = "ward.D2".

Value

An object of class scRNASeq with its clustersSimilarityMatrix and clustersSimiliratyOrdered slots updated.

Author(s)

Ilyess RACHEDI, based on code by Polina PAVLOVICH and Nicolas DESCOSTES.

See Also

plotClustersSimilarity

Examples

## Object scr containing the results of previous steps
load(system.file("extdata/scrFull.Rdat", package="conclus"))
## Calculate clusters similarity
scr <- calculateClustersSimilarity(scr)

ilyessr/conclus documentation built on April 8, 2022, 1:43 p.m.