Seurat cell cycle

This function executes a ubuntu docker that performs seurat cell cycle

seurat_ccycle(
  group = c("sudo", "docker"),
  scratch.folder,
  file,
  separator,
  seed
)

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 first matrix

separator,

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

seed,

integer file necessary for reproducibility

Value

file containing the cluster association in the datasets merged by seurat

Author

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

Examples

if (FALSE) {
library(rCASC)
source("seurat_cCycle.R")
path=getwd()
scratch=paste(path,"/scratch",sep="")
dir.create(scratch)
file1=paste(path,"/setA.csv",sep="")
seurat_ccycle(group="docker", scratch.folder=scratch, file= file1, separator=",",seed=1111)
}