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stephenslab / susieR

R package for "sum of single effects" regression.
https://stephenslab.github.io/susieR
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More informative verbose output #47

Open pcarbo opened 5 years ago

pcarbo commented 5 years ago

It would be nice to get some more informative console output with verbose = TRUE. For example, in the fine-mapping vignette, I get:

> fitted <- susie(finemap$data$X, finemap$data$Y[,1],
                L=5,
                estimate_residual_variance = TRUE,
                scaled_prior_variance = 0.1,
                verbose = TRUE)
[1] "objective:-1384.57253292456"
[1] "objective:-1381.26163424408"
[1] "objective:-1380.75139979919"
[1] "objective:-1380.74854534135"
[1] "objective:-1380.6759533616"
[1] "objective:-1380.67587727196"
[1] "objective:-1377.04794661565"
[1] "objective:-1376.93001122693"
[1] "objective:-1373.29122910603"
[1] "objective:-1373.25708807704"
[1] "objective:-1373.20171636119"
[1] "objective:-1373.20167955938"
[1] "objective:-1373.20062377817"
[1] "objective:-1373.20062375158"
[1] "objective:-1373.20061073365"
[1] "objective:-1373.20061072967"

Some useful data points to show include: which components (1–5) are being updated, the current estimate of the residual variance, the max change in the variational parameters. These could be shown in columns of a table, as in the verbose output of varbvs.