seuratPrior.Rd
This function executes a ubuntu docker that produces a specific number of permutation to evaluate clustering.
seuratPrior( group = c("sudo", "docker"), scratch.folder, file, separator, logTen = 0, seed = 111, PCADim, geneNumber, nCluster, sparse = FALSE, 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 |
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 |
PCADim, | dimensions of PCA for seurat clustering |
geneNumber, | numbers of specific genes for each clusters |
nCluster, | number of cluster analysis. |
sparse, | boolean for sparse matrix |
format, | output file format |
....
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") system("wget ftp://ftp.ensembl.org/pub/release-94/gtf/homo_sapiens/Homo_sapiens.GRCh38.94.gtf.gz") system("gzip -d Homo_sapiens.GRCh38.94.gtf.gz") system("mv Homo_sapiens.GRCh38.94.gtf genome.gtf") scannobyGtf(group="docker", file=paste(getwd(),"bmsnkn_5x100cells.txt",sep="/"), gtf.name="genome.gtf", biotype="protein_coding", mt=TRUE, ribo.proteins=TRUE,umiXgene=3) seuratPrior(group="docker", scratch.folder="/data/scratch/", file=paste(getwd(), "annotated_bmsnkn_5x100cells.txt", sep="/"), separator="\t", logTen=0, seed=111, PCADim=6, geneNumber = 100, nCluster=5) }