permutationClusteringSHARP: Permutations and Clustering

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

Permutations and Clustering

Description

This function executes a ubuntu docker that produces a specific number of permutation to evaluate clustering.

Usage

permutationClusteringSHARP(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  nPerm,
  permAtTime,
  percent,
  separator,
  logTen = 0,
  seed = 1111,
  perplexity = 10
)

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
nPerm	number of permutations to perform the pValue to evaluate clustering
permAtTime	number of permutations that can be computes in parallel
percent	percentage of randomly selected cells removed in each permutation
separator	separator used in count file, e.g. '\t', ','
logTen	1 if the count matrix is already in log10, 0 otherwise
seed	important value to reproduce the same results with same input
perplexity	number of close neighbors for each point. This parameter is specific for tSne. Default value is 10. the performance of t-SNE is fairly robust under different settings of the perplexity. The most appropriate value depends on the density of your data. A larger/denser dataset requires a larger perplexity. Typical values for the perplexity range between 5 and 50

Value

VioPlot of silhouette cells value for each number of cluster used,clusterP file with clustering results for each permutation, killedCell file with removed cells in each permutation, clustering.output a sommarize file with general information for each cells.

Author(s)

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

Examples

## Not run: 
 permutationClusteringSHARP(group="docker",scratch.folder="/home/lucastormreig/CASC2.0/permutationClustering/scratch/",file="/home/lucastormreig/CASC2.0/permutationClustering/Data/TOTAL.csv",nPerm=4,permAtTime=2,percent=10,3,4,separator=",",logTen=0, perplexity, seed=1111)

## End(Not run)

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