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.
[ ] 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
[ ] I updated and/or successfully knitted a vignette that relies on the modified code (which ones?)
[ ] 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.
[ ] I added/removed arguments to a function and updated documentation for all changed/new arguments
[ ] 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)
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.pland responding to the prompts. Test your code after you do this.devtools::document()) and addedNAMESPACEand all other modified files in the root directory and underman.Optional but preferred with PRs
Checklist for New Functions
Required
[ ] I documented my function using ROxygen style.)
[ ] All parameters for the function are described in the documentation and the function has a decriptive title.
Example:
importstatment.Example:
Checklist for changes to existing code
[ ] I added/removed arguments to a function and updated documentation for all changed/new arguments
[ ] 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)