run.SC3: Wraper for running SC3

In Japrin/sscClust: simpler single cell RNAseq data clustering

Wraper for running SC3

Description

Wraper for running SC3

Usage

run.SC3(
  obj,
  assay.name = "exprs",
  out.prefix = NULL,
  n.cores = 8,
  ks = 2:10,
  SC3.biology = T,
  SC3.markerplot.width = 15,
  verbose = F
)

Arguments

obj	object of singleCellExperiment class
assay.name	character; which assay (default: "exprs")
out.prefix	character, output prefix
n.cores	integer, number of cors to use. (default: 8)
ks	integer vector, number of clusters. (default: 2:10)
SC3.biology	logical, SC3 parameter, whether calcualte biology. (default: T)
SC3.markerplot.width	integer, SC3 parameter, with of the marker plot (default: 15)
verbose	logical, whether verbose output. (default: F)

Details

Run SC3 clustering pipeline

Value

an object of SingleCellExperiment class with cluster labels and other info added.

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