Add new functions for loading Manta SV from individual files instead of merges

[rdmorin]

Pull Request Checklists

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Required

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

• [ ] 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.

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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

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

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

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#' 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)

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

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)

[Kdreval]

Is this a draft that you will update or someone should pick it up and complete? Seems like some functions are work in progress, not sure if this is ready for review

[Kdreval]

If the SV functionality was merged in PR #148 , is this PR in the works, or will transform into something else? Just wondering if this should be open, converted into a draft, or closed?

[rdmorin]

I think this was rolled into Adam's PR already

[mattssca]

I think this PR should go into master, The PR I started with the new manta SV functions did not have the other updates added to this PR.

[Kdreval]

I looked over the changes, I think yes not all edits were used in the earlier PR. There are some edits for the new colors and handling of the remote functionality. I think yes it needs to be merged and needs to go to master