seuratPrior: seuratprior

In kendomaniac/CASC: rCASC reproducible Classification Analysis of Single Cell Sequencing Data

seuratprior

Description

This function executes a ubuntu docker that produces a specific number of permutation to evaluate clustering.

Usage

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(s)

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

Examples

## Not run: 
 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)

## End(Not run)

kendomaniac/CASC documentation built on Oct. 4, 2023, 11:10 a.m.