filterCells: Filter cells using either k-means or Dirichlet process means...

In JordanVeldboom/compartmap: A/B compartment inference from ATAC-seq and methylation array data

Description

Filter cells using either k-means or Dirichlet process means clustering of sparsity metrics

Usage

filterCells(
  sparsity.mat,
  rse.obj,
  cluster.method = c("kmeans", "dpmeans"),
  clusters = NULL,
  tol = 0.1,
  plot.data = FALSE,
  invert = FALSE
)

Arguments

sparsity.mat	A matrix of summarized sparsity measures
rse.obj	The unfiltered RangedSummarizedExperiment object
cluster.method	Clustering method to use (default: kmeans)
clusters	How many clusters to generate; if NULL it will autopick the cluster number (default: NULL)
tol	The tolerance or minimum difference in fraction of between cluster sum of squares over total for k-means auto-picking cluster number (default: 0.1)
plot.data	Whether to plot the data
invert	Invert which cluster is used to filter

Value

A filtered RangedSummarizedExperiment object and/or plot of the filtered data

Examples

# FIXME: add example

JordanVeldboom/compartmap documentation built on July 3, 2020, 6:32 p.m.