const-ae
Running logp1 transformation method
Hey thanks for your code. I want to run the logp1 method on my dataset. I am doing it by running --transformation logp1 and --alpha TRUE. Are these two commands correct for running these transformation methods. What should I use for running the acosh transformation. Again thanks a lot and sorry if the questions are too silly.
Best
For a full list of all available transformations, see https://github.com/const-ae/transformGamPoi-Paper/blob/master/benchmark/src/transformations/transformation_helper.R#L333.
But if this is really just about transforming your data, that you have loaded as a SingleCellExperiment object, you would just run
transformGamPoi::acosh_transform(count_matrix)
and for logp1, what about the alpha parameter . Thanks a lot though I think it should just be logp1 and acosh from the file you link.
The alpha is just forwarded to https://github.com/const-ae/transformGamPoi-Paper/blob/master/benchmark/src/transformations/transformation_helper.R#L199