scanpyPermutation: Scanpy Permutation

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

Scanpy Permutation

Description

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

Usage

scanpyPermutation(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  nPerm,
  permAtTime,
  percent,
  separator,
  perplexity,
  pca_number,
  seed = 1111,
  sparse = TRUE,
  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
nPerm	number of permutations to perform the pValue to evaluate clustering
permAtTime	number of permutations that can be computes in parallel
percent	percentage of randomly selected cells removed in each permutation
separator	separator used in count file, e.g. '\t', ','
perplexity	perplexity number for tsne projection, default 10
pca_number	0 for automatic selection of PC elbow.
seed	important value to reproduce the same results with same input
sparse	boolean for sparse matrix
format	output file format csv or txt

Value

To write

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)
 
 seuratBootstrap(group="docker",scratch.folder="/data/scratch/",
      file=paste(getwd(), "annotated_bmsnkn_5x100cells.txt", sep="/"), 
      nPerm=160, permAtTime=8, percent=10, separator="\t",
      logTen=0, pca_number=6, seed=111)

## End(Not run)

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