clusterNgriph: Defining with griph the range of number of clusters to be...

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

Defining with griph the range of number of clusters to be used with SIMLR

Description

This function executes a ubuntu docker that produces a specific number of permutation to evaluate the range of optimal number of clusters using griph algorithm. For more info see rCASC vignette.

Usage

clusterNgriph(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  nPerm,
  permAtTime,
  percent,
  separator,
  logTen = 0,
  seed = 111
)

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
permAtTime	number of permutations that can be computed 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

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 selected as optimal by griph, 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, hist.pdf describing the number of times a specific number of clusters was used during permutations

Author(s)

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

Examples

## Not run: 
 clusterNgriph(group="docker",scratch.folder="/data/scratch/",file=paste(getwd(), "bmsnkn_5x100cells.txt", sep="/"), nPerm=16, permAtTime=8, percent=10, separator="\t",logTen=0, seed=111)

## End(Not run)

kendomaniac/CASC documentation built on June 30, 2024, 3:27 a.m.