wrapperClustersIntegration: integrationCircos

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

integrationCircos

Description

This function execute toprnk analysis which search for correspondence between clusters of two different experiments requires that the data are clustered with any of the software implemented in rCASC, cometsc, bulkClusters and autoencoder4pseudoBulk were already executed.

Usage

wrapperClustersIntegration(
  group = c("sudo", "docker"),
  scratch.folder,
  file.matrix1,
  file.matrix2,
  file.total1,
  file.total2,
  cl1,
  cl2,
  separator1,
  separator2,
  permutation = 100,
  seed = 111,
  top.ranked = 320,
  gsea = "msigdb.all",
  X = 5,
  L = 0.15,
  pvalue = 0.05,
  outputFolder
)

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.matrix1	a character string indicating the path of the first matrix
file.matrix2	a character string indicating the path of the second matrix
file.total1	a character string indicating the path to the total.csv.for the 1st dataset to be integrated. Total.csv is generated with autoencoder4pseudoBulk. File, with file name and extension included.
file.total2	a character string indicating the path to the total.csv.for the 2nd dataset to be integrated. Total.csv is generated with autoencoder4pseudoBulk. File, with file name and extension included.
cl1	path of clustering.output for file.matrix1
cl2	path of clustering.output for file.matrix2
separator1	separator used in count file, e.g. '\t', ','
separator2	separator used in count file, e.g. '\t', ','
permutation	number of permutation to be run
seed	integer file necessary for reproducibility
top.ranked	MAX number of top comet genes to be used for each cluster, default 320
gsea	default msigdb.all, which includes all classes. List of the available GSEA classes: c1.all, c2.cgp, c2.cp.biocarta, c2.cp.kegg, c2.cp.pid, c2.cp.reactome, c2.cp.wikipathways, c3.all, c3.mir, c3.tft.gtrd, c3.tft, c4.cgn, c4.cm, c5.go.bp, c5.go.cc, c5.go.mf, c5.hpo, c6.all, c7.all, c8.all, h.all, msigdb.all. Please note that msigdb.all includes all gsea classes.
X	X parameter for the XLmHG, default 5, for more info please see XLmHG help: https://xl-mhg.readthedocs.io/en/latest/.
L	L parameter for the XLmHG, default 0.15, for more info please see XLmHG help: https://xl-mhg.readthedocs.io/en/latest/.
pvalue	XLmHG pvalue threshold,default 0.05
outputFolder	where results are placed

Value

A picture called integrated_score.png and a file called integrated_score.csv and all the final_scores.csv used to produce the integrated results.

Author(s)

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

Examples

## Not run: 
 library(rCASC)
 wrapperClustersIntegration(group="docker", 
        scratch.folder="/scratch", 
        file.matrix1="/data/clusters_association_paper/setA1_set1/setA1/VandE/VandE.csv",
        file.matrix2="/data/clusters_association_paper/setA1_set1/set1/VandE/VandE.csv",
        cl1="/data/clusters_association_paper/setA1_set1/setA1/VandE/Results/VandE/5/VandE_clustering.output.csv",
        cl2="/data/clusters_association_paper/setA1_set1/set1/VandE/Results/VandE/4/VandE_clustering.output.csv",
        file.total1="/data/clusters_association_paper/setA1_set1/setA1/VandE/Results/setA1/permutation/total.csv",
        file.total2="/data/clusters_association_paper/setA1_set1/set1/VandE/Results/set1/permutation/total.csv",
        separator1=",", separator2=",", 
        permutation=100, seed=111, top.ranked=320, gsea="msigdb.all", X=5, L=0.15, pvalue=0.05,
        outputFolder="/data/clusters_association_paper/setA1_set1"
        )

## End(Not run)

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