NEWS.md

In ashr: Methods for Adaptive Shrinkage, using Empirical Bayes

ashr v2.0

Major Changes

There are a few major changes in output and input that will likely break existing dependencies. Here are the highlights

• the main output (lfsr, lfdr, etc) is rearranged into a dataframe, called result.

  • so, for example, the lfsr is now a$result$lfsr instead of a$lfsr

  • or, better, use the accessor function get_lfsr(a) to extract the lfsr etc

• I added accessor functions get_lfsr, get_lfdr, get_pm, get_psd etc to access the lfsr, lfdr, posterior mean and posterior standard deviation. Using these functions to access results will help ensure your code remains valid if I happen to change the internal structure of the results again (although not anticipated...)

• output fitted.g is renamed fitted_g, and flash.data becomes flash_data to make the whole package convention more consistent. Also fit becomes fit_details.

• function prefixes comppost and compdens replaced with comp_post and comp_dens, again for consistency.

• nonzeromode option is replaced with the option mode to specify mode. Or use mode="estimate" to estimate the mode.

• more flexible control of output. For example, you can say you want only the logLR output by specifying outputlevel = c("lfsr","logLR"), or only posterior mean by outputlevel = c("PosteriorMean").

ashr documentation built on Aug. 22, 2023, 1:07 a.m.