View source: R/scanpyBootstrap.R
scanpyBootstrap | R Documentation |
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 |
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
## Not run:
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")
## End(Not run)
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