scanpyBootstrap.Rd
This function executes a ubuntu docker that produces a specific number of permutation using scanpy as clustering tool.
scanpyBootstrap( group = c("sudo", "docker"), scratch.folder, file, nPerm, permAtTime, percent, separator, perplexity = 40, pca_number = 50, seed = 111, format = "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 |
separator, | separator used in count file, e.g. '\t', ',' |
perplexity, | perplexity value for tsne projection |
pca_number, | PCA threshold selected using seuratPCAEval function. |
seed, | important value to reproduce the same results with same input |
format, | output file format csv or txt. Mandatory because scanpy only accepts sparse matrices |
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") scanpyBootstrap(group="docker",scratch.folder="/data/scratch/", file=paste(getwd(), "matrix.mtx", sep="/"), nPerm=160, permAtTime=8, percent=10, separator="\t", perplexity=10, pca_number=6, seed=111, format="txt") }