A function to handle sigle cell Lorenz Quality filter for Single-cells

This function executes a docker that embeds Lorenz filter from Diaz at al. Bioinformatics 2016

lorenzFilter(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  p_value,
  separator
)

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. IMPORTANT: full path to the file MUST be included

p_value,

lorenz statistics threshold, suggest value 0.05, i.e. 5% probability that the cell of low quality is selected

separator,

separator used in count file, e.g. '\t', ','

Value

The output is a filtered counts table. Output will be in the same format and with the same separator of input.

Author

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

Examples

if (FALSE) {
        system("wget http://130.192.119.59/public/testSCumi_mm10.csv.zip")
     library(rCASC)
     system("unzip testSCumi_mm10.csv.zip")
     #filtering low quality cells
     lorenzFilter(group="docker",scratch.folder="/data/scratch/", 
                  file=paste(getwd(),"testSCumi_mm10.csv", sep="/"),
                  p_value=0.05, separator=',')
}