gseaXLmHG: gseaXLmHG

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

gseaXLmHG

Description

This function execute XLmHG estimation of the presence of enriched GSEA class in cluster-specific genes detected by COMET for the clusters of two independent datasets and uses this information to search for correspondence between clusters in the two independent datasets. This function requires that the two datasets have been clustered in rCASC and COMET analysis was run.

Usage

gseaXLmHG(
  group = c("sudo", "docker"),
  scratch.folder,
  xCometFolder,
  yCometFolder,
  gsea = c("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"),
  X,
  L,
  pvalue,
  separatorX,
  separatorY,
  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
xCometFolder	path of Comet results from X experiment
yCometFolder	path of Comet results from Y experiment
gsea	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, we suggest to use this dataset for a complete analysis.
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
separatorX	separator used in count file, e.g. '\t', ','
separatorY	separator used in count file, e.g. '\t', ','
outputFolder	the folder where GSEA folder will be created

Value

A folder called GSEA with all the results generated. The function produces an integrated output, final_score.csv, of the results obtained for progressively increasing length of the cluster-specific-genes detected by COMET.

Author(s)

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

Examples

## Not run: 
 library(rCASC)
 gseaXLmHG(group="docker",
        scratch.folder="/scratch", 
        xCometFolder="/data/reanalysis_on_AIsc/comparing_CRC0327/NT_CTX/CRC0327_NT_2_clx/VandE/Results/VandE/8/outputdata",
        yCometFolder="/data/reanalysis_on_AIsc/comparing_CRC0327/NT_CTX/CRC0327_cetux_2_clx/VandE/Results/VandE/8/outputdata",
        gsea="c2.cp.kegg",
        X=5,
        L=0.15,
        pvalue=0.05,
        separatorX=",",
        separatorY=",",
        outputFolder="/data/reanalysis_on_AIsc/comparing_CRC0327/NT_CTX"
 )

## End(Not run)

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