permAnalysisSeurat: Permutation Analysis Seurat

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

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