tsneBootstrap: Executing clustering with tSne

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

Executing clustering with tSne

Description

This function executes a ubuntu docker that produces a specific number of permutation using tSne as clustering tool.

Usage

tsneBootstrap(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  nPerm,
  permAtTime,
  percent,
  range1,
  range2,
  separator,
  logTen = 0,
  seed = 111,
  sp = 0.8,
  clusterPermErr = 0.05,
  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 be executed
permAtTime	number of permutations computed in parallel
percent	percentage of randomly selected cells removed in each permutation
range1	beginning of the range of clusters to be investigated
range2	end of the range of clusters to be investigated
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, default is 111
sp	minimun number of percentage of cells that has to be in common in a cluster, between two permutations, default 0.8
clusterPermErr	probability error in depicting the number of clusters in each permutation, default = 0.05
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

A folder Results containing a folder with the name of the experiment, which contains: VioPlot of silhouette cells value for each number of cluster used, a folder with the number of clusters used for SIMLR clustering, which contains: 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: 
system("wget http://130.192.119.59/public/section4.1_examples.zip")
unzip("section4.1_examples.zip")
setwd("section4.1_examples")
tsneBootstrap(group="docker",scratch.folder="/data/scratch/",file=paste(getwd(), "bmsnkn_5x100cells.txt", sep="/"), nPerm=160, permAtTime=8, percent=10, range1=4, range2=6, separator="\t",logTen=0, seed=111, sp=0.8, clusterPermErr=0.05, perplexity=10)

## End(Not run)

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