cleanCluster: Clean clusters

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Clean clusters

Description

Filter cells that exceed N median absolute deviations from cluster center in UMAP coordinate space. Assumes that Seurat::FindClusters() has already been run.

Usage

cleanCluster(object, mad.threshold = 3, return.plots = F, verbose = T)

Arguments

object	Seurat object.
mad.threshold	Filter threshold. Represents minimal number of median absolute deviations from median required to omit cell from object. Default is 3.
return.plots	Logical indicating whether to return plots. If true, returns list containing object along with ggplot handles. If false, only filtered object is returned.
verbose	Logical indicating whether to print progress messages.

Value

list (return.plots == T) or seurat object (return.plots == F)

Author(s)

Nicholas Mikolajewicz

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.