This function executes a ubuntu docker that remove the effect of cell cycle from a single cells dataset

ccRemove(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  separator,
  seed = 111,
  cutoff = 3,
  species,
  rawCount
)

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 folder where input data are located and where output will be written and matrix name "/bin/users/matrix.csv"

separator,

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

seed,

is important to reproduce the same results with the same input

cutoff,

a cut-off equal to 3 is almost equal to 0.05 p.value

species,

human or mouse

rawCount,

1 for raw 0 otherwise

Value

return a normalized matrix, whith prefix LS_cc_, in which cell cycle effect is removed

Examples

if (FALSE) { system("wget http://130.192.119.59/public/annotated_lorenz_testSCumi_mm10.csv.zip") unzip("annotated_lorenz_testSCumi_mm10.csv.zip") ccRemove(group="docker" , scratch.folder="/data/scratch", file=paste(getwd(),"annotated_lorenz_testSCumi_mm10.csv", sep="/"), separator=",", seed=111, cutoff=3, species="mouse", rawCount=1) }