cvSOUP: Cross validation for SOUP

In lingxuez/SOUP: Semi-soft Clustering of Single Cell Data

Description

Cross validation for SOUP

Usage

cvSOUP(expr, type = "log", Ks = c(2:10), nfold = 10, nCV = 10,
  mc.cores = 1, ext.prop = NULL, pure.prop = 0.5, seeds = NULL,
  verbose = TRUE)

Arguments

expr	A cell-by-gene expression matrix, either the raw counts or log-transformed expressions.
type	"log" if expr has been normalized and log-transformed (default), or "count" (default) expr contains the raw counts.
Ks	A sequence of cluster numbers
nfold	(optional) Number of folds, default is 10
nCV	(optional) Number of repetitions, default is 10
mc.cores	(optional) Number of cores for parallelization, default is 1 without parallelization
seeds	(optional) A list of seeds to be used, with length nCV, default is NULL
verbose	(optional) Whether to print progress, default is TRUE

lingxuez/SOUP documentation built on May 28, 2019, 3:38 p.m.