clusterExperimentWorkflow: Performs clustering workflow using 'clusterExperiment'...

In BIMSBbioinfo/netSmooth: Network smoothing for scRNAseq

Description

Performs clustering workflow using 'clusterExperiment' functions

Usage

clusterExperimentWorkflow(
  se,
  dimReduceFlavor = c("pca", "tsne", "dm", "umap"),
  cluster.ks = 5:10,
  cluster.function = "pam",
  nVarDims = c(100, 500, 1000),
  makeConsensusProportion = 0.7,
  makeConsensusMinSize = 4,
  runMergeClusters = TRUE,
  is.counts = TRUE,
  random.seed = 1
)

Arguments

se	SummarizedExperiment object
dimReduceFlavor	algorithm for reduced dimension embedding step
cluster.ks	range of Ks to cluster over
cluster.function	clustering algorithm to use for all clusterings
nVarDims	numbers of variable genes to perform clusterings over
makeConsensusProportion	proportion of times samples need to be co-clustered for co-clustering step
makeConsensusMinSize	minimum cluster size
runMergeClusters	logical: merge similar clusters
is.counts	logical: is data counts
random.seed	passed to clusterExperiment. set to NULL in order to not set a random seed.

Value

cluster assignments

BIMSBbioinfo/netSmooth documentation built on Dec. 24, 2019, 8:08 p.m.