nClusterEvaluationSIMLR: Evaluation of the numbur of optimal clusters

View source: R/nClusterEvaluationSIMLR.R

nClusterEvaluationSIMLRR Documentation

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