genesSelection.Rd
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 )
group, | a character string. Two options: sudo or docker, depending to which group the user belongs |
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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. |
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Luca Alessandri, alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino
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) }