ValidateClusters: Cluster Validation

In mayer-lab/SeuratForMayer2018: Seurat : R Toolkit for Single Cell Genomics

Description

Methods for validating the legitimacy of clusters using classification. SVMs are used as the basis for the classification. Merging is done based on the connectivity from an SNN graph.

Usage

ValidateClusters(object, pc.use = NULL, top.genes = 30,
  min.connectivity = 0.01, acc.cutoff = 0.9, verbose = TRUE)

Arguments

object	Seurat object
pc.use	Which PCs to use to define genes in model construction
top.genes	Use the top X genes for each PC in model construction
min.connectivity	Threshold of connectedness for comparison of two clusters
acc.cutoff	Accuracy cutoff for classifier
verbose	Controls whether to display progress and merging results

Value

Returns a Seurat object, object@ident has been updated with new cluster info

mayer-lab/SeuratForMayer2018 documentation built on May 25, 2019, 9:34 p.m.