seuratPrior: seuratprior

In kendomaniac/rCASC: 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/rCASC documentation built on July 3, 2024, 6:05 a.m.