[Bioc-devel] How I hide non-exported function from the manual

[Vincent Carey]

On Wed, Jun 3, 2020 at 11:48 PM stefano <mangiolastefano using gmail.com> wrote:

> Hello Community,
>
> I am used to document function although hey are not exported
>
>
I suppose you are talking about tidybulk?  I am somewhat mystified by the
behavior
of

%vjcair> R CMD build tidybulk

* checking for file ‘tidybulk/DESCRIPTION’ ... OK

* preparing ‘tidybulk’:

* checking DESCRIPTION meta-information ... OK

* installing the package to process help pages

* building the PDF package manual

Hmm ... looks like a package

Converting Rd files to LaTeX .................

Creating pdf output from LaTeX ...


which produces a 147 page manual, and as you note many

non-user-visible symbols are documented in manual.  I've

never seen the "process help pages" phase in any

of my packages, and I don't know why.


I don't have experience with the RdMacros setting in

DESCRIPTION, and the way S3 methods are being handled

in the package leads, I think, to an excess of Rd

files relative to what you have as visible symbols

in the package namespace.


Perhaps some tidyverse experts can comment.


> ```
> #' Get differential transcription information to a tibble using edgeR.
> #'
> #' @import dplyr
> #' @import tidyr
> #' @import tibble
> #' @importFrom magrittr set_colnames
> #' @importFrom stats model.matrix
> #' @importFrom utils installed.packages
> #' @importFrom utils install.packages
> #' @importFrom purrr when
> #'
> #'
> #' @param .data A tibble
> #' @param .formula a formula with no response variable, referring only to
> numeric variables
> #' @param .sample The name of the sample column
> #' @param .transcript The name of the transcript/gene column
> #' @param .abundance The name of the transcript/gene abundance column
> #' @param .contrasts A character vector. See edgeR makeContrasts
> specification for the parameter `contrasts`. If contrasts are not present
> the first covariate is the one the model is tested against (e.g., ~
> factor_of_interest)
> #' @param method A string character. Either "edgeR_quasi_likelihood" (i.e.,
> QLF), "edgeR_likelihood_ratio" (i.e., LRT)
> #' @param significance_threshold A real between 0 and 1
> #' @param minimum_counts A positive integer. Minimum counts required for at
> least some samples.
> #' @param minimum_proportion A real positive number between 0 and 1. It is
> the threshold of proportion of samples for each transcripts/genes that have
> to be characterised by a cmp bigger than the threshold to be included for
> scaling procedure.
> #' @param fill_missing_values A boolean. Whether to fill missing
> sample/transcript values with the median of the transcript. This is rarely
> needed.
> #' @param scaling_method A character string. The scaling method passed to
> the backend function (i.e., edgeR::calcNormFactors;
> "TMM","TMMwsp","RLE","upperquartile")
> #' @param omit_contrast_in_colnames If just one contrast is specified you
> can choose to omit the contrast label in the colnames.
> #'
> #' @return A tibble with edgeR results
> #'
> get_differential_transcript_abundance_bulk <- function
> [...]
> ```
>
> However this leads to 2 problems
>
> 1) The PDF manual includes many function that are not accessible to the
> user. How can I hide documented non-exported function from the manual
> 2) I receive the Biocheck note. "You have <TO_MANY> initialised objects".
> Again how can I document an object without initialising it?
>
> Thanks a lot.
>
> Best wishes.
>
> *Stefano *
>
>
>
> Stefano Mangiola | Postdoctoral fellow
>
> Papenfuss Laboratory
>
> The Walter Eliza Hall Institute of Medical Research
>
> +61 (0)466452544
>
>         [[alternative HTML version deleted]]
>
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