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rcavalcante / DMRcate

Custom version of DMRcate package
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DMR identification on limma time-course analysis in mice #3

Open dtzhu337 opened 7 months ago

dtzhu337 commented 7 months ago

Hi there,

We have a longitudinal study where plasma sample from mice at multiple age were subjected to Illumina Methylation array. In this case, we would like to identify differential methylated CpGs (DMCs) that globally changed over the time-course, hence, we used limma time-course analysis with the intra-block correlation based block on mouse ID. We then would like to identify DMRs using dmrcate function. However, I found that the time course analysis was not a case included in the function. I understand the idea of the DMRs identification is to identify genomic regions where DMCs enriched in. Any suggestion on how I can modify the functions within the package to achieve this, especially how to indicate mice methylation array data and time-course analysis (limma)? Thank you in advance.

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rcavalcante commented 7 months ago

Hi,

I'm sorry, but I'm not the official maintainer of this package. See #1. I made this repo because I needed to make some alterations for my own purposes and wanted to save the result. I suppose I should make the repo private.

Thanks, Raymond