Seurat Permutation

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

seuratPermutation(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  nPerm,
  permAtTime,
  percent,
  separator,
  logTen = 0,
  pcaDimensions,
  seed = 1111,
  sparse = FALSE,
  format = "NULL",
  resolution = 0.6
)

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', ','

logTen,

1 if the count matrix is already in log10, 0 otherwise

pcaDimensions,

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

resolution,

resolution for Seurat Analysis

Value

To write

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)
 
 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, pcaDimensions=6, seed=111)
}