permAnalysisSeurat: Permutation Analysis Seurat

View source: R/permAnalysisSeurat.R

permAnalysisSeuratR Documentation

Permutation Analysis Seurat

Description

This function analyze the data that came up from permutationClustering script.

Usage

permAnalysisSeurat(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  nCluster,
  separator,
  sp = 0.8,
  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

nCluster,

number of cluster that has to be analyzed

separator,

separator used in count file, e.g. '\t', ','

sp,

minimun number of percentage of cells that has to be in common between two permutation to be the same cluster.

sparse,

boolean for sparse matrix

format,

output file format csv or txt

Value

stability plot for each nCluster,two files with score information for each cell for each permutation.

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, pcaDimensions=6, seed=111, format="NULL")

## End(Not run)

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