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

[stefano]

Hello Community,

I am used to document function although hey are not exported

```
#' 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

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