nClusterEvaluationSIMLR: Evaluation of the numbur of optimal clusters

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

Evaluation of the numbur of optimal clusters

Description

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

Usage

nClusterEvaluationSIMLR(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  range1,
  range2,
  separator,
  logTen,
  nPerm,
  percent,
  rangeFile
)

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
range1,	First number of cluster that has to be analyzed
range2,	Last number of cluster that has to be analyzed
separator,	separator used in count file, e.g. '\t', ','
logTen,	0 for raw count, 1 otherwise
nPerm,	how many times number of cluster will be evaluated
percent,	number of cells that has to be removed for bootstrap
rangeFile,	name of the file that has for each row each number of cluster that has to be analyzed

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: 
permAnalysis("docker","path/to/scratch","path/to/data/TOTAL",3,4,",",0.8)#

## End(Not run)

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