R/get_names.R

In ytakemon/GINIR: Genetic inteRaction and EssenTiality neTwork mApper

#' Get unique DepMap-compatible gene IDs
#' 
#' @description 
#' `get_GeneNameID()` and `get_DepMapID()` provide tools for converting gene symbols/ids and 
#' common cell line aliases to DepMap's unique gene name and cell line identifiers, respectively.
#' 
#' @param gene_name string containing a vector of either Hugo gene symbol or numeric NCBI ID
#' @param data_dir string Path to GINIR_data
#' @return string
#' 
#' @import rlang
#' @import dplyr
#' @import utils
#' 
#' @export
#' @examples
#' gretta_data_dir <- './GRETTA_example/'
#' gretta_output_dir <- './GRETTA_example_output/'
#' 
#' if(!dir.exists(gretta_data_dir)){
#'   download_example_data(".")
#' }
#' 
#' get_GeneNameID('A1CF', data_dir = gretta_data_dir)
#' 
get_GeneNameID <- function(gene_name, data_dir) {
  if (is.null(data_dir)) {
    stop("No directory to data was specified. Please provide path to DepMap data.")
  }
  if (!dir.exists(data_dir)) {
    stop("DepMap data directory does not exists. ",
         "Please check again and provide the full path to the DepMap data directory.")
  }
  
  # Load necessary data
  dep_annot <- CCLE_exp_annot <- NULL  # see: https://support.bioconductor.org/p/24756/
  load(paste0(data_dir, "/dep_annot.rda"), envir = environment())
  load(paste0(data_dir, "/CCLE_exp_annot.rda"), envir = environment())
  load(paste0(data_dir, "/copy_num_annot.rda"), envir = environment())
  
  # For Hugo symbols/NCBI IDs - from dependency
  # prob.
  if (any(dep_annot$GeneNames %in% gene_name | dep_annot$GeneID %in%
          gene_name)) {
    res <- dep_annot %>%
      dplyr::filter(.data$GeneNames %in% gene_name |
                      .data$GeneID %in% gene_name) %>%
      dplyr::pull(.data$GeneNameID)
    
    # For Hugo IDs - from CCLE RNA-seq expr.
  } else if (any(CCLE_exp_annot$GeneNames %in% gene_name |
                 CCLE_exp_annot$GeneID %in% gene_name)) {
    res <- CCLE_exp_annot %>%
      dplyr::filter(.data$GeneNames %in% gene_name |
                      .data$GeneID %in% gene_name) %>%
      dplyr::pull(.data$GeneNameID)
    
  # For Hugo IDs - from CN data.
  } else if (any(copy_num_annot$GeneNames %in% gene_name |
               copy_num_annot$GeneID %in% gene_name)) {
  res <- copy_num_annot %>%
    dplyr::filter(.data$GeneNames %in% gene_name |
                    .data$GeneID %in% gene_name) %>%
    dplyr::pull(.data$GeneNameID)
  
  # If no matches are found
  } else {
    stop("Cannot find gene name. Please check the spelling. ",
         "Gene names should be a valid Hugo Symbol and in all caps!")
  }
  return(res)
}

#' @describeIn get_GeneNameID Get unique DepMap-compatible sample IDs
#' @param sample_name string containing a vector of unique sample_id used in proteomics data or common cell line names
#' @param data_dir string Path to GINIR_data
#' @return string
#' 
#' @import rlang
#' @import dplyr
#' @import utils
#' 
#' @export
#' @examples
#' gretta_data_dir <- './GRETTA_example/'
#' gretta_output_dir <- './GRETTA_example_output/'
#' 
#' if(!dir.exists(gretta_data_dir)){
#'   download_example_data(".")
#' }
#' 
#' get_DepMapID('JURKAT', data_dir = gretta_data_dir)
#' 
get_DepMapID <- function(sample_name, data_dir) {
  # Load necessary data
  protein_annot <- sample_annot <- NULL  # see: https://support.bioconductor.org/p/24756/
  load(paste0(data_dir, "/protein_annot.rda"), envir = environment())
  load(paste0(data_dir, "/sample_annot.rda"), envir = environment())
  
  # For sample names from proteomics data
  if (any(protein_annot$GygiNames %in% sample_name)) {
    res <- protein_annot %>%
      dplyr::filter(.data$GygiNames %in% sample_name) %>%
      dplyr::pull(.data$DepMap_ID)
    
    # For sample names that are commonly used
    # in the wild
  } else if (any(sample_annot$stripped_cell_line_name %in%
                 sample_name)) {
    res <- sample_annot %>%
      dplyr::filter(.data$stripped_cell_line_name %in%
                      sample_name) %>%
      dplyr::pull(.data$DepMap_ID)
    
    # If no matches are found
  } else {
    stop("Cannot find sample. ",
         "Please check the spelling. ",
         "Common sample names should be all caps without spaces or special symbols!")
  }
  return(res)
}