unstableFiltering: unstableFiltering

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

unstableFiltering

Description

This function executes a ubuntu docker that remove cells on the basis of their cell stability score.

Usage

unstableFiltering(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  nCluster,
  separator,
  sThreshold
)

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
nCluster,	number of clusters
separator,	separator used in count file, e.g. '\t', ','
sThreshold,	cell stability score threshold, a value between 0 and 1.

Value

A filtered counts file

Author(s)

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

Examples

## Not run: 
unstableFiltering(group="docker", scratch.folder="/media/lucastormreig/8799-82B32/PHD/CASC8.1Stable/CASC8.0STABLE/new/unstableFiltering/scratch/", file="/media/lucastormreig/8799-82B32/PHD/CASC8.1Stable/CASC8.0STABLE/new/unstableFiltering/data/testset.txt",nCluster=5, separator="\t",sThreshold=0.75)

## End(Not run)

kendomaniac/CASC documentation built on Oct. 4, 2023, 11:10 a.m.