Question: How to customized CpGlist or Genelist in chAMP.gsea
0
gravatar for sugus
12 months ago by
sugus40
China Pharmaceutical University
sugus40 wrote:

Hi there,

I am trying to use chAMP pipeline to analysis EPIC methylation data. In the chAMP pipeline, there is an embeded GSEA module called chAMP.gsea and it seems to support customized CpGlist or Genelist from its help document. (see the following CpGlist and Genelist)

Usage

    champ.GSEA(beta=myNorm,
               DMP=myDMP[[1]],
               DMR=myDMR,
               CpGlist=NULL,
               Genelist=NULL,
               pheno=myLoad$pd$Sample_Group,
               method="fisher",
               arraytype="450K",
               Rplot=TRUE,
               adjPval=0.05)
Arguments

beta    
A matrix of values representing the methylation scores for each sample (M or B). Better to be imputed and normalized data. (default = myNorm)
DMP 
Results from champ.DMP() function. (default = myDMP)
DMR 
Results from champ.DMR() function. (default = myDMR)
CpGlist 
Apart from previous parameters, if you have any other CpGs list want to do GSEA, you can input them here as a list. (default = NULL)
Genelist    
Apart from previous parameters, if you have any other Gene list want to do GSEA. you can inpute them here as a list. (default = NULL)
pheno   
If use ebayes method, user needs to provide phenotype information to conduct global test. (default = myLoad$pd$Sample_Group)
method  
Which method would be used to do GSEA?"gometh" or "fisher". (default = "gometh")
arraytype   
Which kind of array your data set is? (default = "450K")
Rplot   
If gometh method was chosen, should Probability Weight plot will be plotted. More information please check gometh package. (default = TRUE)
adjPval 
Adjusted p value cutoff for all calculated GSEA result. (default = 0.05)

However, there isn't an example for how to use these two parameters and my code is as following:

dmg.enhancer <- dmp.res[which(dmp.res$deltaBeta <= (-0.2) & dmp.res$adj.P.Val < 0.05 & dmp.res$isEnhancer == TRUE),"gene"]; dmg.enhancer <- dmg.enhancer[which(dmg.enhancer != "")]

load(file = file.path(resDir.NOFILTER.C1vsC2,"myNorm.rda"))
load(file = file.path(resDir.NOFILTER.C1vsC2,"myDMP.rda"))
load(file = file.path(resDir.NOFILTER.C1vsC2,"myDMR.rda"))
load(file = file.path(resDir.NOFILTER.C1vsC2,"myLoad.rda"))
Genelist <- list(); Genelist[["dmg.enhancer"]] <- dmg.enhancer
tmp <- champ.GSEA(Genelist = Genelist,arraytype = "EPIC")

Following is the demo of my Genelist:

> Genelist
$`dmg.enhancer`
   [1] "EPHB2"        "LYRM1"        "NUAK2"        "CEP170"       "DICER1"       "FNIP1"        "MAST2"        "C5orf22"      "HIPK2"       
  [10] "TTC7B"        "NT5DC1"       "TRIO"         "C3orf26"      "TTC7B"        "FOXP1"        "SNX2"         "C2orf86"      "PDE4D"

And I got the error all the time:

[===========================]
[<<<< ChAMP.GSEA START >>>>>]
-----------------------------
Error in if (names(Genelist) == NULL | lengthis.na(names(Genelist))) !=  : 
  argument is of length zero

If there is anyone could give me some hint or an example of how to use these two parameters.

Thanks there

champ gsea • 512 views
ADD COMMENTlink written 12 months ago by sugus40
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1429 users visited in the last hour