collate_igblast_results function

[mannycruz]

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Checklist for all PRs

Required

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

`

sample_table <- read_tsv("/projects/nhl_meta_analysis_scratch/gambl/results_local/shared/gambl_genome_results.tsv")
sample_table <- collate_igblast_results(sample_table = sample_table)
[1] "Searching for MiXCR results in directory:/projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/mixcr-1.2/01-mixcr/genome/"
[1] "Removing empty entries"
[1] "Removing rows that exceed missing threshold"
[1] "Joining tables"
Joining, by = "biopsy_id"
`

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

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Checklist for New Functions

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• 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:

#' 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

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• 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)

[rdmorin]

Some suggestions for how to improve efficiency and generalize

[rdmorin]

Parameters that are specific to functions being called by collate_results should really not be passed to them from this function. It's going to get too messy as the collate_ family grows. Remove from here but leave them as available parameters in the new function.

[rdmorin]

Update docs after you make this optional so the users know they only need to specify it if they want to override the default

[rdmorin]

Update code above to ensure the unix_group is always present in the samples table

[rdmorin]

Start with a directory listing to avoid a loop. You probably will have to do this twice (once for each unix group). I think another recently added collate function does something similar

[Kdreval]

@mannycruz is this ready to go or is it still in development?

[mannycruz]

@Kdreval Ready to go!