GAMBLR Improvements - truncated lines in manual, posted issues, README, new portal.R functions.

[mattssca]

This PR is addressing the following items;

1. Fixing examples that previously had >100 characters per line (causing the examples to be truncated in the PDF manual).

2. Proposing a fix for reported issue #179.

3. Adding a "100 characters line" example to the new-function template in the README.

4. The golden standard function documentation example has been updated to actually reflect the best practices detailed in the previous section (in the README).

5. New functions added to portal.R. This includes four new functions;

   • custom_caselist - Lets the user specify a case list from a set of sample IDs.

   • get_study_info - Useful for retrieving study-specific identifiers, allowing for easier maintenance of existing studies, updating existing studies, etc.

   • cbioportal_create - A new helper function that wraps all the other study-specific functions with the same parameters (as defined in this function). Preventing inconsistencies in these identifiers, and also allows for a more straightforward execution for setting up cBioPortal studies. Note, this function is not exported (internal function).

   • setup_expression_data - This function gathers expression data and prepares it into a format that is accepted by cBioPortal. For more details on how this function operates, see the function documentation.

6. All package documentation has been re-generated, reflecting the latest changes detailed above.

Pull Request Checklists

Important: When opening a pull request, keep only the applicable checklist and delete all other sections.

Checklist for all PRs

Required

• [x] I tested the new code for my use case (please provide a reproducible example of how you tested the new functionality)

• [x] I ensured all dplyr functions that commonly conflict with other packages are fully qualified.

This can be checked and addressed by running check_functions.pl and responding to the prompts. Test your code after you do this.

• [x] I generated the documentation and checked for errors relating to the new function (e.g. devtools::document()) and added NAMESPACE and all other modified files in the root directory and under man.

Optional but preferred with PRs

• [x] I updated and/or successfully knitted a vignette that relies on the modified code (which ones?)

Checklist for New Functions

Required

• [x] I documented my function using ROxygen style.)

• [x] All parameters for the function are described in the documentation and the function has a decriptive title.

Example:

#' Use GISTIC2.0 scores output to reproduce maftools::chromoplot with more flexibility
#'
#' @param scores output file scores.gistic from the run of GISTIC2.0
#' @param genes_to_label optional. Provide a data frame of genes to label (if mutated). The first 3 columns must contain chromosome, start, and end coordinates. Another required column must contain gene names and be named `gene`. (truncated for example)
#' @param cutoff optional. Used to determine which regions to color as aberrant. Must be float in the range [0-1]. (truncated for example)

• [ ] My function uses a library that isn't already a dependency of GAMBLR and I made the package aware of this dependency using the function documentation import statment.

Example:

#' @return nothing
#' @export
#' @import tidyverse ggrepel

Checklist for changes to existing code

• [x] I added/removed arguments to a function and updated documentation for all changed/new arguments

• [x] I tested the new code for compatability with existing functionality in the Master branch (please provide a reprex of how you tested the original functionality)

[mattssca]

This PR is now ready for review.

Besides what's described above, this PR also includes the following updates;

• Fix for issue #185

• Many updates to examples in function docs. The majority of these changes include fixes that allow pkgdown::build_site to successfully execute all the examples and generate function-specific HTML documents. other updates include writing fully reproducible examples and preventing man/*.Rd files to be generated for helper/internal functions.

• Minor updates to fancy_vignette, again, allowing for examples to be executed within the pkgdown::build_site command.

• Updates to get_manta_sv (issue #188). This update includes a change in the logic of this function. For more details, see the described issue. Another parameter was also added to this function (verbose) to let the user control if read messages should be printed to the console or not. The default behavior is verbose = TRUE (to honor the existing behavior of this function). All functions that internally call get_manta_sv has also been updated with respect to the new parameter. The same goes for the vignettes.

• Fix for issue #189