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cozygene / BayesCCE

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alpha priors #1

Closed fifdick closed 5 years ago

fifdick commented 6 years ago

Hi,

I have some questions for using the BayesCCE that i could not answer myself by going through the documentation provided in bayescce.m . I am planning to use your tool on whole genome bisulfite sequencing data, where I derive the desired beta values from read coverage on each CpG position. Now my question is, how do I derive the alpha prior that I need to provide to the function? As I am working on brain tissue, I thought I could use data that you have referenced in your publication: https://doi.org/10.4161/epi.23924 as a reference and derive the priors from this. Is this possible and if so, how would I proceed? It is unclear for me how and if I need to use this https://github.com/tminka/fastfit package, as you recommended in your README. Looking forward to your answer.

Fiona

E-R commented 6 years ago

Once you have a matrix with cell counts from external data (each row corresponds to an individual and each column corresponds to a cell type), to get alpha you just need to run the polya_fit function (using fasfit) on it.