Permutation Analysis

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

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

Luca Alessandri , alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino

Examples

if (FALSE) {
permAnalysis("docker","path/to/scratch","path/to/data/TOTAL",3,4,",",0.8)#
}