R/readGistic.R

In Niinleslie/MesKit: A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic alterations

# extract recurrent CNA genes from gistic file
readGisticGene <- function(gisticGenesFile = NULL, Gistic_type = NULL){
  
  if(!is.null(gisticGenesFile)){
    gisticGenes <- data.table::fread(input = gisticGenesFile, stringsAsFactors = FALSE, header = TRUE)
    if(is.na(unique(gisticGenes[, ncol(gisticGenes), with = FALSE])[1])){     
      gisticGenes <- gisticGenes[,-ncol(gisticGenes), with = FALSE]
    }
    
    #wide peak boundaries
    wpb <- as.character(gisticGenes[3]) 
    wpb <- wpb[2:length(wpb)]
    
    # keep the information of peak boundaries and genes 
    gisticGenes <- gisticGenes[c(4:nrow(gisticGenes)),]
    gisticGenes$cytoband <- gsub(pattern = ' ', replacement = '_', x = gisticGenes$cytoband)
    colnames(gisticGenes) <- c( 'cytoband', paste0( colnames(gisticGenes)[2:length(colnames(gisticGenes))], '_',wpb))
    
    gisticGenes <- suppressWarnings(data.table::melt(gisticGenes, id.vars = 'cytoband'))
    gisticGenes <- gisticGenes[!gisticGenes$value %in% '']
    
    #gisticGenes <- gisticGenes[!grep(pattern = '|', x = gisticGenes$value, fixed = TRUE)] #remove genes with ambiguous annotation
    gisticGenes <- gisticGenes  %>% 
      dplyr::select("variable", "value") %>%
      tidyr::separate(col = "variable", into = c("Cytoband", "Wide_Peak_Boundaries"), 
                      sep = "_", remove = TRUE) %>%
      dplyr::mutate(Gene=sub("\\|.+", "", .data$value), Gistic_type = Gistic_type) %>%
      dplyr::select(-"value")
    
    return(gisticGenes)
  }
}

## read GISTIC all_lesions files
readGisticAllLesions <- function(gisticAllLesionsFile = NULL, verbose = TRUE){
  if(verbose){
    cat(paste0('--Processing ', basename(gisticAllLesionsFile), '\n'))
  }
  
  gisticLesions <- data.table::fread(input = gisticAllLesionsFile, stringsAsFactors = FALSE, header = TRUE)
  if(is.na(unique(gisticLesions[, ncol(gisticLesions), with = FALSE])[1])){     
    gisticLesions <- gisticLesions[,-ncol(gisticLesions), with = FALSE]
  }
  
  gisticLesions <- gisticLesions %>%
    dplyr::select(1,2,3,6) %>%
    `colnames<-` (c("PeakID", "Cytoband", "WPB", "Qvalue")) %>%
    dplyr::filter(!grepl("values", .data$PeakID)) %>%
    dplyr::rowwise() %>%
    dplyr::mutate(WPB = strsplit(.data$WPB, split = "(", fixed =  TRUE)[[1]][1]) %>%
    dplyr::mutate(Gistic_type = substr(.data$PeakID, start = 1, stop = 3), PeakID = NULL) %>% as.data.table()
  
  return(gisticLesions)
}