reduce.cluster: Reduce redundant clusters of AP clustering

In JiekaiLab/SOT: Single-cell Orientation Tracing

Description

Merge highly related clusters into groups

Usage

reduce.cluster(
  sce,
  datatype = "logcounts",
  genes.use = "genes.use",
  projections = "l2",
  method = "pearson",
  sim = NULL,
  center = TRUE,
  scale. = TRUE,
  normalize.score = TRUE,
  ncore = 2,
  ...
)

Arguments

sce	A SingleCellExperiment object.
datatype	Sepcify the data type in sce for filtering.
method	The method to calculate the affinity matrix, can be pearson (Defult) or cosine.
center	Center the expression before performing PCA - default is FALSE.
scale.	Scale the expression before performing PCA - default is FALSE.
normalize.score	Whether to normalize pc1 score.
ncore	Number of cores used for parallel.
...	Additional arguments passed on to apcluster
dsim	Prior defined similarty matrix of lv1.score for clustering - default is NULL.

Value

• Group labels of genes

• Basic stats of Groups

• Eigengenes

JiekaiLab/SOT documentation built on Jan. 25, 2022, 3:14 p.m.