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
[ ] I updated and/or successfully knitted a vignette that relies on the modified code (which ones?)
[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.
[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_samplesget_ssm_by_sampleget_gambl_metadataadd_icgc_metadata (internal function for get_gambl_metadata)
get_gambl_outcomes (internal function for get_gambl_metadata)
get_combined_svget_manta_svget_sample_cn_segmentsget_coding_ssmannotate_ssm_blacklistcollate_resultsassign_cn_to_ssmget_ssm_by_regionget_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.
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.devtools::document()
) and addedNAMESPACE
and all other modified files in the root directory and underman
.Optional but preferred with PRs
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:
import
statment.Example:
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
, andget_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.