Problems encountered when using on the server

[FM-Jewl]

Dear professor, when I use the latest R package "TransBioInfoLab/coMethDMR" on the server, it always cames with error: " could not find function...". The following is the log：

library(coMethDMR) Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) Registered S3 methods overwritten by 'lme4': method from cooks.distance.influence.merMod car influence.merMod car dfbeta.influence.merMod car dfbetas.influence.merMod car data(betasChr22_df) data(pheno_df) CpGisland_ls <- readRDS(

• system.file (
• "extdata",
• "CpGislandsChr22_ex.RDS",
• package = 'coMethDMR',
• mustWork = TRUE
• ) ) coMeth_ls <- CoMethAllRegions (
• dnam = betasChr22_df,
• betaToM = TRUE, #converts to mvalues
• CpGs_ls = CpGisland_ls,
• arrayType = "450k",
• returnAllCpGs = FALSE,
• output = "CpGs"
• ) Error in CoMethAllRegions(dnam = betasChr22_df, betaToM = TRUE, CpGs_ls = CpGisland_ls, : could not find function "CoMethAllRegions"

It would be much appropriate if you can teach me about this. Thank you in advance.

[gabrielodom]

We are working on this issue right now, and we hope to have it fixed within the next few days. Also, please transition to our lab-maintained package version at https://github.com/TransBioInfoLab/coMethDMR. You can install this version with

install_github("TransBioInfoLab/coMethDMR", ref = "devel")

[alanajones]

Hi,

I was also having the same issue with "could not find function '__'", so I switched to the alternative package above. I was able to run it without any errors, the log file looked fine, etc. However, in my results, I had no beta estimates or standard errors and all my p-values & FDRs = 1 for any region. I tried 3 different models x 4 different traits and still got the same output for all. Even in previous runs when the models didn't converge and p=1, I've still gotten an effect estimate for that row. Here's the code I ran and a screenshot of the output below. Any thoughts on what could be happening here? Thanks.

fit <- lmmTestAllRegions( betas = x, region_ls = z, y, contPheno_char = phenotypes, covariates_char = fixedcov, modelType = "randCoef", arrayType = "EPIC", outLogFile = paste0("lmmLog", Sys.Date(), ".txt") )

out <- AnnotateResults( lmmRes_df = fit, arrayType = "EPIC" )

write.table(out, file =out.file,sep=",",quote=FALSE,col.names=T,row.names=FALSE,na="")

[gabrielodom]

Hi Ms. Jones, Please forgive me for taking so long to reply. Could you send us a samples of your data so we can try to replicate this issue? We have a lab meeting this afternoon, and we will discuss this problem then. Thank you! Gabriel

[alanajones]

Hi Gabriel,

Apologies for my late response. Since this is our collaborator’s data, we don’t necessarily feel comfortable sharing it without going through a more formal process (e.g., DUA). However, I’d be happy to set up a Zoom call to in which I could share my screen and we can troubleshoot. Then again, this may be a moot point if the issue with the package has already been resolved. I haven’t run it in a few weeks and can try it again if there have been updates.

Thanks, Alana From: Gabriel J. Odom @.> Date: Monday, April 5, 2021 at 10:23 AM To: lissettegomez/coMethDMR @.> Cc: Jones, Alana @.>, Comment @.> Subject: Re: [lissettegomez/coMethDMR] Problems encountered when using on the server (#6)

Hi Ms. Jones, Please forgive me for taking so long to reply. Could you send us a samples of your data so we can try to replicate this issue? We have a lab meeting this afternoon, and we will discuss this problem then. Thank you! Gabriel

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/lissettegomez/coMethDMR/issues/6#issuecomment-813451681, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ASTBZAAK7DLLIZTPH57IP33THHIXXANCNFSM4ZU6TXUA.

[gabrielodom]

Can we set up a Zoom call then? When are you available?

[alanajones]

That’d be great. Wednesday and Friday mornings (before 12 CST) are good for me.

Alana

From: Gabriel J. Odom @.> Date: Thursday, April 15, 2021 at 3:35 PM To: lissettegomez/coMethDMR @.> Cc: Jones, Alana @.>, Comment @.> Subject: Re: [lissettegomez/coMethDMR] Problems encountered when using on the server (#6)

Can we set up a Zoom call then? When are you available?

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[gabrielodom]

Friday morning works for me. Can you email me (so I can send you a meeting invite)? gabriel.odom@fiu.edu

[gabrielodom]

Hi @alanajones, @fveitz and I tracked down the issue on my computer, and she is currently working to confirm on hers. We believe the issue is that R munged the sample IDs in your betas dataset. We see that they all start with "X", while the sample IDs in your pheno dataset do not. This could be caused by R prohibiting column names of a data frame from starting with numbers. We worked around this by adding "X" to all the sample IDs in pheno, and we were able to get estimates, standard errors, and p-values.

Fernanda is confirming this now, and we will be adding a check in our functions to stop users if their sample IDs don't match. In the mean time, please update the sample IDs in pheno to match what appears in betas. Also, for good measure, please install the most recent version of the package. We fixed a bunch of other documentation issues.

[fveitz]

Hi @alanajones and @gabrielodom, I confirm this is the issue. When I re-run on my computer, I got the same results: chrom start end nCpGs Estimate StdErr Stat pValue 1 chr16 2961485 2961799 6 -0.001313689 0.0007835092 -1.676673 0.0936064

[alanajones]

Ok I will update the package and sample IDs and rerun. Thank you both for your help @gabrielodom @fveitz!

Alana

[gabrielodom]

@alanajones, please let us know if you run into other issues. @fveitz, we will close this issue once we've added a check for sample IDs