seuratprior

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"
)

Arguments

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

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

Value

....

Author

Luca Alessandri, alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino

Examples

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)
}