On Wed, Jun 3, 2020 at 10:40 PM Vincent Carey
<st...@channing.harvard.edu> wrote:
>
> On Wed, Jun 3, 2020 at 11:48 PM stefano <mangiolastef...@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.
This step happens iff you have \Sexpr{} macros in your man/*.Rd files
(see
https://github.com/wch/r-source/blob/5bd6e3ce1430374105ebf02101f9d55173496cfe/src/library/tools/R/build.R#L582-L586)
/Henrik
>
>
> 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]]
> >
> > _______________________________________________
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> --
> The information in this e-mail is intended only for th...{{dropped:6}}
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