ap.cluster: Affinity propagation clustering

Description Usage Arguments Value

View source: R/clustering.R

Description

AP clustering on genes and calculate the eigengenes of each cluster

Usage

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

Arguments

sce

A SingleCellExperiment object or matrix.

datatype

Specify the data type in sce for filtering.

genes.use

Specify the genes to perform clustering.

projections

Whether to calculate reconstructions and scores using the L1 norm ("l1") the L2 norm ("l2").

sim

Prior defined similarty matrix of genes for clustering - default is NULL.

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

Wheter to normalize the pc1 score.

minsize

Minimum cluster size.

ncore

Number of cores used for parallel.

...

Additional arguments passed on to apcluster

Value


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