unstableFiltering — unstableFiltering • rCASC

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

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

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

Examples

if (FALSE) {
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)
}