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perishky / meffil

Efficient algorithms for analyzing DNA methylation data.
Artistic License 2.0
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Possible to include all minfi's cell type references in the meffil.estimate.cell.counts.from.betas function? #24

Closed Lei-Guo closed 3 years ago

Lei-Guo commented 4 years ago

The current function only estimates cell types in blood/saliva. Could you please also include the brain (DLPFC) cell type reference (from minfi) in this function?

perishky commented 4 years ago

Hi Lei-Guo,

Sorry about the wait. I haven't been monitoring this closely enough. I've recently added this, it is named "guintivano dlpfc".

Matt

perishky commented 4 years ago

Hi Samuel,

This particular cell count reference is obtained by combining a white blood cell type reference (GEO dataset: GSE35069https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE35069) with a buccal cell type reference (the buccal DNA methylation profiles from GEO dataset GSE48472https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48472). It assumes that the cell content of saliva is a mix of white blood cells and buccal epithelial cells.

You could use this for either buccal samples or saliva samples.

Best, Matt

From: Samuel Carleial notifications@github.com Sent: 21 October 2020 8:37 AM To: perishky/meffil meffil@noreply.github.com Cc: Matthew Suderman matthewsuderman@hotmail.com; Comment comment@noreply.github.com Subject: Re: [perishky/meffil] Possible to include all minfi's cell type references in the meffil.estimate.cell.counts.from.betas function? (#24)

Hi Matt, to my understanding, this is one of the few, if not the only, function in R that can estimate cell counts for saliva samples specifically (besides GLINT perhaps?). I have a study in which I want to estimate cell counts from saliva samples. I noticed that in the abovementioned function there is the reference called "saliva gse48472".

I assume this should not be used for both saliva and buccal cells, but only saliva, correct? Could you then give me more information on that cell-type reference, and whether there is a reference study/publication that report it?

I would appreciate it very much, because I am planing to use your function in my pipeline. *Maybe one suggestion would be to add this information in the documentation of the package.

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samuel-carleial commented 4 years ago

Hi Matt, I found that out also inside your code. Thank you for the feedback!