Need to use the S4 generic `plogis()` from DelayedArray. It's default method is `stats::plogis()`, so it does the right thing.
Peter Hickey authored on 28/06/2018 16:27:46
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@@ -19,7 +19,7 @@ importFrom(BiocGenerics, "anyDuplicated", "cbind", "colnames", |
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importFrom(stats, "approxfun", "fisher.test", "ppoints", |
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"predict", "preplot", "qchisq", |
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"qnorm", "qqplot", "qunif", "cov2cor", |
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- "plogis", "setNames") |
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+ "setNames") |
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importFrom(graphics, "abline", "axis", "layout", "legend", "lines", |
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"mtext", "par", "plot", "points", "polygon", "rect", "rug", "text") |
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import(parallel) |
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@@ -341,8 +341,6 @@ BSmooth <- function(BSseq, |
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# TODOs ------------------------------------------------------------------------ |
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-# TODO: The @trans slot isn't getting correctly set (it's using stats::plogis |
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-# instead of DelayedArray::plogis). |
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# TODO: Use the logging facilities of BiocParallel. This is a longterm goal. |
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# For example, we could set custom messages within .BSmooth() using the |
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# futile.logger syntax; see the BiocParalell vignette 'Errors, Logs and |