run.SC3: Wraper for running SC3

run.SC3R Documentation

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 Dec. 15, 2022, 1:04 p.m.