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Bioconductor / RaggedExperiment

Matrix-like representations of mutation and CN data
https://bioconductor.org/packages/RaggedExperiment
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unclear documentation of qreduceAssay #5

Closed lwaldron closed 7 years ago

lwaldron commented 7 years ago

Arguments given at the top of ?qreduceAssay:

qreduceAssay(x, query, simplify, i = 1, withDimnames = TRUE,
  background = NA)

but further below it says: qreduceAssay: A function accepting arguments score, range, and qrange:

mtmorgan commented 7 years ago

This is meant to be describing the definition of simplify when used in qreduceAssay(); the indentation implies this when the help is viewed as plain text; how are you viewing the help page?

lwaldron commented 7 years ago

It's indented correctly to be a part of simplify (in RStudio). What I didn't get (and still am not sure I get) is that the simplify argument of qreduceAssay is a function of two functions, disjoinAssay, and qreduceAssay. The section on disjoinAssay shows a simplify=mean and simplify(values), and I guess from that I got stuck thinkingsimplify=mean was a valid choice. Still, the example below shows simplify having three arguments, rather than two?

mtmorgan commented 7 years ago

Its trying to say that simplify when it is an argument to disjoinAssay() behaves like mean(), whereas when it's an argument to qreduceAssay() it takes three arguments. I guess these should be renamed disjoinSimplify and qreduceSimplify or similar to disambiguate.

LiNk-NY commented 7 years ago

I vote for simplifyDisjoin and simplifyReduce because at least they will start with simplify. Thoughts? @mtmorgan @lwaldron Making changes... now :)