search

epigen / RnBeads

Git working Repo synced to the Bioconductor: http://bioconductor.org/packages/devel/bioc/html/RnBeads.html
https://rnbeads.org/
7 stars 8 forks source link

Setting options for RnBeads: cell-type and diff. methylation for continuous data #13

Open samuel-carleial opened 3 years ago

samuel-carleial commented 3 years ago

Hi,

I could not find this information in the documentation or at online foruns. I would like to know if when setting rnb.options() is there a way to specify sample tissue (specifically saliva).

Additionally, when defining differential methylation, can we set variables which are not categorical, but instead continuous? I would like to associate methylation with a psychological sumscore scale.

Thank you.

schmic05 commented 3 years ago

Hi,

No, there is not direct option to specify the cell type. However, you could use the cell type as a covariate in the differential analysis using the option covariate.adjustment.columns.

Unfortunately, RnBeads does not support continuous outputs in the differential analysis. You might want to have a look at the limma R package (http://bioconductor.org/packages/release/bioc/html/limma.html) for that.