genesPrioritization.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/simlrGeneProritization.R
\name{genesPrioritization}
\alias{genesPrioritization}
\title{Gene prioritization with SIMLR}
\usage{
genesPrioritization(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  nPerm,
  permAtTime,
  percent,
  nCluster,
  separator,
  logTen = 0,
  seed = 111,
  sp = 0.8,
  clusterPermErr = 0.05
)
}
\arguments{
\item{group, }{a character string. Two options: sudo or docker, depending to which group the user belongs}

\item{scratch.folder, }{a character string indicating the path of the scratch folder}

\item{file, }{a character string indicating the path of the file, with file name and extension included}

\item{nPerm, }{number of permutations to be executed}

\item{permAtTime, }{number of permutations computed in parallel}

\item{percent, }{percentage of random cells removed in each permutation}

\item{nCluster, }{the number of clusters, where to run prioritization}

\item{separator, }{separator used in count file, e.g. '\\t', ','}

\item{logTen, }{1 if the count matrix is already in log10, 0 otherwise}

\item{seed, }{important value to reproduce the same results with same input}

\item{sp, }{minimun number of percentage of cells that has to be in common in a cluster, between two permutations, default 0.8}

\item{clusterPermErr, }{probability error in depicting the number of clusters in each permutation, default = 0.05}
}
\value{
VioPlot of silhouette cells value for each number of cluster used,clusterP file with clustering results for each permutation, killedCell file with removed cells in each permutation, clustering.output a sommarize file with general information for each cells.
}
\description{
This function executes a ubuntu docker that produces a specific number of permutation to evaluate clustering and identify the genes that play the major role in clustering.
}
\examples{
\dontrun{
system("wget http://130.192.119.59/public/section4.1_examples.zip")
unzip("section4.1_examples.zip")
setwd("section4.1_examples")
genesPrioritization(group="docker",scratch.folder="/data/scratch/",file=paste(getwd(), "bmsnkn_5x100cells.txt", sep="/"), nPerm=160, permAtTime=8, percent=10, nCluster=5, separator="\t", logTen=0, seed=111, sp=0.8, clusterPermErr=0.05)
}

}
\author{
Luca Alessandri, alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino
}