Adding error messages to functions that reads from local files.

[mattssca]

Pull Request Checklists

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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.

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• [ ] 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)

PR Comments

This PR includes error messages for the following functions; get_ssm_by_samples get_ssm_by_sample get_gambl_metadata add_icgc_metadata (internal function for get_gambl_metadata) get_gambl_outcomes (internal function for get_gambl_metadata) get_combined_sv get_manta_sv get_sample_cn_segments get_coding_ssm annotate_ssm_blacklist collate_results assign_cn_to_ssm get_ssm_by_region get_excluded_samples

The above-mentioned functions have all been tested on remote GAMBLR and all return the added error message if Sys.setenv(R_CONFIG_ACTIVE = "remote" has not been specified.

Functions have also been tested after specifying the config to remote, and the collection of the above-mentioned functions runs the intended way, except for; get_combined_sv, get_sample_cn_segments, and get_ssm_by_region. I am currently looking into why the files needed for these functions are not accessible when running GAMBLR remote with a VPN connection.

Other small updates in this PR include typos in the README as well as removing trailing white spaces.

[rdmorin]

Is this ready for re-review?

[mattssca]

Yes, it's ready.

[rdmorin]

OK. Can you also please respond to my question above?

[mattssca]

This PR has now been updated based on the latest review comments, in this commit.