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ben-laufer / DMRichR

A R package and executable for the preprocessing, statistical analysis, and downstream testing and visualization of differentially methylated regions (DMRs) from CpG count matrices (Bismark cytosine reports)
https://www.benlaufer.com/DMRichR/
MIT License
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Can I use this package for RRBS data & issue with running DMRichR::DM.R #76

Closed MiaSands closed 11 months ago

MiaSands commented 11 months ago

Hello,

Thank you for developing this convenient package for defining DMRs!

My first question is that if this package applies to RRBS data.

My second question is that I tried to run the following code: DMRichR::DM.R(genome=c("mm10"),testCovariate = "Treatment", adjustCovariate = c("Exposure"), sexCheck = FALSE, cores = 20, coverage = 2, perGroup = 0.75, minCpGs = 5,cutoff = 0.05,EnsDb = FALSE, GOfuncR = TRUE,cellcompostion = FALSE).

I kept getting the error "Error in DMRichR::DM.R(genome = c("mm10"), testCovariate = "Treatment", : unused argument (cellcompostion = FALSE)".

Do you have any advice for how to resolve this error?

Thank you for your time!

ben-laufer commented 11 months ago

Hi @MiaSands, can you remove the cellcomposition argument and give the latest version of DMRichR a try?

Also, the package does work with RRBS data. You many need to optimize the parameters in the call to dmrseq() based on the discussions in the issues section of the dmrseq GitHub and omit the blocks section.

MiaSands commented 11 months ago

Thanks for the advice. I fixed the problem by reinstalling R and I will give it a try on my RRBS data.