clusterStability: 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

clusterStability(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  nPerm,
  range1 = 3,
  range2 = 3,
  separator,
  logTen = 0,
  clustering,
  perplexity = 10,
  pcaDimensions,
  seed = 1111
)

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
range1	first number of cluster for k means algorithm
range2	last number of cluster for k means algorithm
separator	separator used in count file, e.g. '\t', ','
logTen	1 if the count matrix is already in log10, 0 otherwise
clustering	clustering method to use : "SIMLR" , "tSne", "griph"
perplexity	Number of close neighbors for each point. This parameter is specific for tSne. Default value is 10.Setting this parameter when use a clustering method different by tSne will be ignored.
pcaDimensions	dimensions to use for pca reduction for Seurat
seed	important value to reproduce the same results with same input

Value

plot with cluster stability

Author(s)

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

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