ccRemove: Cc remove

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

Cc remove

Description

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

Usage

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

Author(s)

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

Examples

## Not run: 
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)

## End(Not run)

kendomaniac/rCASC documentation built on July 3, 2024, 6:05 a.m.