seuratIntegrationPermutation: Seurat Integration Permutation

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

Seurat Integration Permutation

Description

This function executes a ubuntu docker that performs seurat integration to identify associated clusters in two independent experiment. The analysis is repeated mutiple times removing 10

Usage

seuratIntegrationPermutation(
  group = c("sudo", "docker"),
  scratch.folder,
  file1,
  file2,
  separator1,
  separator2,
  cl1,
  cl2,
  permutation,
  seed,
  outputFolder,
  K = 0.8
)

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
file1	a character string indicating the path of the first matrix
file2	a character string indicating the path of the second matrix
separator1	separator used in count file, e.g. '\t', ','
separator2	separator used in count file, e.g. '\t', ','
cl1	path of clustering.output for file1
cl2	path of clustering.output for file2
permutation	number of permutation for statistic
seed	integer file necessary for reproducibility
outputFolder	path to the output folder
K	resolution for seurat analysis

Value

A folder called ISC, the input data, the intermediate results and a comma separated file final_score.csv summarising the frequency by which the seuratIntegration function return a an integration cluster including at least 50

Author(s)

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

Examples

## Not run: 
seuratIntegrationPermutation(group="docker", scratch.folder="/home/user/scratch", file1="/home/user/dockerFile/Seurat_join_DAPUSHARE/function/example/set1.csv",file2="/home/user/dockerFile/Seurat_join_DAPUSHARE/function/example/setA.csv", separator1=",",separator2=",",cl1=, cl29,permutation=100, seed=111) 

## End(Not run)

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