R/extract_prot.R

In ytakemon/GINIR: Genetic inteRaction and EssenTiality neTwork mApper

#' @title Extract protein expression data for given cell lines
#' 
#' @description FUNCTION_DESCRIPTION
#' 
#' @param input_samples string A vector of DepMap_ID(s) must be provided, Default: NULL
#' @param input_genes string Optional Hugo Symbol(s) encoding proteins of interest, Default: NULL
#' @param data_dir string Path to GINIR_data
#' @return Data frame containing protein expression for samples provided in the input. 
#' If no genes were specified, the function will return a data frame of proteins profiled in DepMap
#' 
#' @details See also `extract_protein_rna` to extract proteomics profile data
#' 
#' @examples 
#' gretta_data_dir <- './GRETTA_example/'
#' gretta_output_dir <- './GRETTA_example_output/'
#' 
#' if(!dir.exists(gretta_data_dir)){
#'   download_example_data(".")
#' }
#' 
#' extract_prot(
#' input_samples = c('ACH-000004', 'ACH-000146'), 
#' input_genes = c('CIC'),
#' data_dir = gretta_data_dir)
#' 
#' @rdname extract_prot
#' @export 
#' @importFrom dplyr select contains left_join filter
#' @importFrom tidyr pivot_longer

extract_prot <- function(input_samples = NULL, input_genes = NULL,
                         data_dir = NULL) {
  
  # Print and check to see input was provided
  if (is.null(input_samples)) {
    stop("No samples given. Please input sample DepMap_ID")
  }
  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
  protein_annot <- protein_nodup <- sample_annot <- NULL  # see: https://support.bioconductor.org/p/24756/
  load(paste0(data_dir, "/sample_annot.rda"), envir = environment())
  load(paste0(data_dir, "/protein_nodup.rda"), envir = environment())
  load(paste0(data_dir, "/protein_annot.rda"), envir = environment())
  
  # Check if inputs are recognized
  if (!all(input_samples %in% sample_annot$DepMap_ID)) {
    stop(input_samples[!input_samples %in% sample_annot$DepMap_ID],
         ", not recognized as a valid sample")
  }
  if (!all(input_genes %in% protein_nodup$Gene_Symbol)) {
    stop(input_genes[!input_genes %in% protein_nodup$Gene_Symbol],
         ", not recognized or protein expression is not available. Please check spelling or remove gene name from input")
  }
  
  # If no input gene is given, give full expr
  # table
  if (is.null(input_genes)) {
    res <- protein_nodup %>%
      dplyr::select(.data$Gene_Symbol, .data$Description,
                    .data$Uniprot, .data$Uniprot_Acc, dplyr::contains("_TenPx")) %>%
      tidyr::pivot_longer(-c(.data$Gene_Symbol,
                             .data$Description, .data$Uniprot, .data$Uniprot_Acc),
                          names_to = "Gygi_ID", values_to = "protein_expr") %>%
      dplyr::left_join(protein_annot, by = c(Gygi_ID = "GygiNames")) %>%
      dplyr::select(.data$DepMap_ID, dplyr::everything())
    
    return(res)
  }
  
  # Otherwise, provide only expr of genes of
  # interst
  res <- protein_nodup %>%
    dplyr::filter(.data$Gene_Symbol %in% input_genes) %>%
    dplyr::select(.data$Gene_Symbol, .data$Description,
                  .data$Uniprot, .data$Uniprot_Acc, dplyr::contains("_TenPx")) %>%
    tidyr::pivot_longer(-c(.data$Gene_Symbol, .data$Description,
                           .data$Uniprot, .data$Uniprot_Acc), names_to = "Gygi_ID",
                        values_to = "protein_expr") %>%
    dplyr::left_join(protein_annot, by = c(Gygi_ID = "GygiNames")) %>%
    dplyr::filter(.data$DepMap_ID %in% input_samples,
    ) %>%
    dplyr::select(.data$DepMap_ID, dplyr::everything())
  
  # Notify if some samples do not have
  # expression data
  if (!all(input_samples %in% res$DepMap_ID)) {
    GRETTA_says <- paste0("Following sample did not contain protein data: ",
                          paste0(input_samples[!input_samples %in%
                                                 res$DepMap_ID], collapse = ", "))
    message(GRETTA_says)
    return(res)
  } else {
    return(res)
  }
}