Preparing `beer `input from raw read count tables

[FarzanehRah]

Hi, I am working with phip-seq dataset and have a raw read count table that I would like to use as input for the beerfunctions. Could you please provide guidance on how to prepare the input for use with the beerpackage from a raw read count table, also steps for normalizing the data? Thanks

[athchen]

beer functions start with a PhIPData object. Example code to construct a PhIPData object from a raw read count table can be found in the PhIPData vignette linked here.

Once the data is prepared in the PhIPData format, data normalization and modeling are all performed with the beer or edgeR function depending on your data precision requirements (beer gives more accurate estimates of enrichment but may take longer depending on the number of peptides in the library. beer can be parallelized to run on groups of peptides (such as by viruses). edgeR is much faster to run on large libraries but is less accurate for detecting smaller fold-changes of enrichment.).

[FarzanehRah]

Thank you for taking the time to explain all the details!