Cell Cycle

This function executes a ubuntu docker that associates to each cell a cell cycle stage

cellCycle2(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  separator,
  G1_a,
  G1_b,
  S_a,
  S_b,
  G2M_a,
  G2M_b,
  seed = 111
)

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', ','

G1_a,

starting point in time series for G1 phase

G1_b,

ending point in time series for G1 phase

S_a,

starting point in time series for S phase

S_b,

ending point in time series for S phase

G2M_a,

starting point in time series for G2M phase

G2M_b,

ending point in time series for G2M phase

seed,

important parameter for reproduce the same result with the same input

Value

will change all the files generated from permAnalysis algorithm in a new folder matrixName_Cluster_merged/

Author

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

Examples

if (FALSE) {
#getwd(link)
#unzipFolder
scratch.folder=paste(getwd(),"/scratch",sep="")
file=paste(getwd(),"/data/annotated_Buettner.csv",sep="")
 cellCycle2(group="docker",scratch.folder,file,separator=",",G1_a=22,G1_b=23,S_a=22,S_b=23,G2M_a=85,G2M_b=86,seed=111)
}