permAnalysis: Permutation Analysis

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

Permutation Analysis

Description

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

Usage

permAnalysis(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  range1,
  range2,
  separator,
  sp,
  clusterPermErr = 0.05,
  maxDeltaConfidence = 0.01,
  minLogMean = 0.05
)

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', ','
sp,	minimun number of percentage of cells that has to be in common between two permutation to be the same cluster.
clusterPermErr,	error that can be done by each permutation in cluster number depicting.Default = 0.05
maxDeltaConfidence,	max value for Delta confidence for genes feature selection
minLogMean,	min value for Log mean for genes feature selection

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.