Gene prioritization with SIMLR

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.

genesPrioritization(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  nPerm,
  permAtTime,
  percent,
  nCluster,
  separator,
  logTen = 0,
  seed = 111,
  sp = 0.8,
  clusterPermErr = 0.05
)

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 file, with file name and extension included

nPerm,

number of permutations to be executed

permAtTime,

number of permutations computed in parallel

percent,

percentage of random cells removed in each permutation

nCluster,

the number of clusters, where to run prioritization

separator,

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

logTen,

1 if the count matrix is already in log10, 0 otherwise

seed,

important value to reproduce the same results with same input

sp,

minimun number of percentage of cells that has to be in common in a cluster, between two permutations, default 0.8

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.

Author

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

Examples

if (FALSE) {
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)
}