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.

Examples

if (FALSE) { system("wget http://130.192.119.59/public/testSCumi_mm10.csv.zip") library(casc) 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=',') }