simlrBootstrap.Rd
This function executes a ubuntu docker that produces a specific number of permutation with SIMLR clustering.
simlrBootstrap( group = c("sudo", "docker"), scratch.folder, file, nPerm, permAtTime, percent, range1, range2, separator, logTen = 0, seed = 111, sp = 0.8, clusterPermErr = 0.05, maxDeltaConfidence = NULL, minLogMean = NULL )
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 |
nPerm, | number of permutations to be executed |
permAtTime, | number of permutations computed in parallel |
percent, | percentage of randomly selected cells removed in each permutation |
range1, | beginning of the range of clusters to be investigated |
range2, | end of the range of clusters to be investigated |
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 |
maxDeltaConfidence, | max value for Delta confidence for genes feature selection |
minLogMean, | min value for Log mean for genes feature selection |
A folder Results containing a folder with the name of the experiment, which contains: VioPlot of silhouette cells value for each number of cluster used, a folder with the number of clusters used for SIMLR clustering, which contains: 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
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") simlrBootstrap(group="docker",scratch.folder="/data/scratch/",file=paste(getwd(), "bmsnkn_5x100cells.txt", sep="/"), nPerm=160, permAtTime=8, percent=10, range1=4, range2=6, separator="\t",logTen=0, seed=111, sp=0.8, clusterPermErr=0.05) }