ssc.clust: Perform clustering using reduced data

In Japrin/sscClust: simpler single cell RNAseq data clustering

Perform clustering using reduced data

Description

Perform clustering using reduced data

Usage

ssc.clust(
  obj,
  assay.name = "exprs",
  method.reduction = "iCor",
  method = "kmeans",
  k.batch = 2:6,
  method.vgene = "HVG.sd",
  SNN.k = 10,
  SNN.method = "eigen",
  SC3.biology = T,
  SC3.markerplot.width = 15,
  dpclust.rho = NULL,
  dpclust.delta = NULL,
  parlist = NULL,
  out.prefix = NULL,
  seed = NULL,
  ncore = NULL,
  ...
)

Arguments

obj	object of singleCellExperiment class
assay.name	character; which assay (default: "exprs")
method.reduction	character; which dimention reduction method to be used, should be one of "iCor", "pca" and "none". (default: "iCor")
method	character; clustering method to be used, should be one of "kmeans", "hclust", "dynamicTreeCut", "SNN", "dpclust", "adpclust" and "SC3". (default: "kmeans")
k.batch	integer; number of clusters to be evaluated. (default: 2:6)
method.vgene	character; variable gene identification method used. (default: "HVG.sd")
SNN.k	integer; number of shared NN. (default: 10)
SNN.method	character; cluster method applied on SNN, one of "greedy", "eigen", "infomap", "prop", "louvain", "optimal", "spinglass", "walktrap", "betweenness", "leiden". (default: "eigen")
SC3.biology	logical, SC3 parameter, whether calcualte biology. (default: T)
SC3.markerplot.width	integer, SC3 parameter, with of the marker plot (default: 15)
dpclust.rho	numberic; cuttoff of rho, if it is NULL, infer frome the data (default: NULL)
dpclust.delta	numberic; cuttoff of delta, if it is NULL, infer frome the data (default: NULL)
parlist	list; if not NULL, use th parameters in it. (default: NULL)
out.prefix	character; output prefix, if not NULL, some plots of intermediate result will be produced. (default: NULL)
seed	integer; seed of random number generation. (default: NULL)
ncore	integer; nuber of CPU cores to use. if NULL, automatically detect the number. (default: NULL)
...	parameters pass to clustering methods

Details

If no dimension reduction performed or method is "none", expression data of variable genes, which can be speficed by method.vgene, will be used for clustering. Otherwise, the reduced data specified by method.reduction will be used. The cluster label will stored in the colData of the object of singleCellExperiment class, with colname in the format of {method.reduction}.{method}k{k} where {k} get value(s) from k.batch.

Value

an object of SingleCellExperiment class with cluster labels added.

Japrin/sscClust documentation built on May 23, 2024, 7:12 a.m.