cellCycle2: Cell Cycle

In kendomaniac/CASC: rCASC reproducible Classification Analysis of Single Cell Sequencing Data

Cell Cycle

Description

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

Usage

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(s)

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

Examples

## Not run: 
#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)

## End(Not run)

kendomaniac/CASC documentation built on Oct. 4, 2023, 11:10 a.m.