ccRemove.Rd
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 )
group, | a character string. Two options: sudo or docker, depending to which group the user belongs |
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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 |
return a normalized matrix, whith prefix LS_cc_, in which cell cycle effect is removed
Luca Alessandri , alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino
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) }