wrapperMixModelsUmap: wrapperMixModelsUmap

In kendomaniac/rCASC: rCASC reproducible Classification Analysis of Single Cell Sequencing Data

wrapperMixModelsUmap

Description

This function executes a ubuntu docker that performs wrapperMixModelsUmap

Usage

wrapperMixModelsUmap(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  geneList,
  separator,
  k,
  seed,
  epochs,
  finalName,
  maxit = 10000
)

Arguments

group	a character string. Two options: sudo or docker, depending to which group the user belongs
scratch.folder	a character string indicating the path of the scratch folder
file	a character string indicating the path of the count matrix
geneList	a character string indicating the path of the geneList matrix (no header, no row names)
separator	separator used in count file, e.g. '\t', ','
k	number of soft labels to divide the density
seed	number for reproducibility
epochs	epochs number for umap algorithm
finalName	name for output files
maxit	number of max iteration for mixmodels

Value

plot

Author(s)

Luca Alessandri, alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino

Examples

## Not run: 
dir.create("scratch")
wrapperMixModelsUmap(group=c("docker"), scratch.folder=paste(getwd(),"/scratch",sep=""), file=paste(getwd(),"/setA.csv",sep=""),separator=",",seed=111,epochs=1000,k=3,finalName="prova",geneList=paste(getwd(),"/geneList.csv",sep=""))

## End(Not run)

kendomaniac/rCASC documentation built on July 3, 2024, 6:05 a.m.