Genes selection from genesPrioritization output

This function executes a ubuntu docker that extracts the genes playin major role in clusterin from output of genesPrioritization

genesSelection(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  nCluster,
  separator,
  seed = 111,
  sp = 0.8,
  clusterPermErr = 0.05,
  maxDeltaConfidence = 0.01,
  minLogMean = 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

nCluster,

the number of clusters, where to run prioritization

separator,

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

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

maxDeltaConfidence,

max value for Delta confidence for gene prioritization p-values.

minLogMean,

min value for Log mean gene prioritization p-value. P-value indicates the importance of a gene in defining clusterization.

Value

....

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")
genesSelection(group="docker",scratch.folder="/data/scratch/",file=paste(getwd(), "bmsnkn_5x100cells.txt", sep="/"), nCluster=5, separator="\t",  seed=111, sp=0.8, clusterPermErr=0.05, maxDeltaConfidence=0.01, minLogMean=0.05)
}