fix FL cohort and use transformation status for tFL-study case set

[rdmorin]

Pull Request Checklists

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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)

• 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

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• I documented my function using ROxygen style.)

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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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