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

Description Usage Arguments Value

View source: R/clusterExperimentWorkflow.R

Description

Performs clustering workflow using 'clusterExperiment' functions

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
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.