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. 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 the ...{{dropped:18}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel