nobuild/annotate_drivers.R

In caravagnalab/CNAqc: CNAqc - Copy Number Analysis quality check

#' #' Title
#' #'
#' #' @param x
#' #' @param drivers_list
#' #' @param function_column
#' #' @param gene_column
#' #'
#' #' @return
#' #' @export
#' #'
#' #' @examples
#' annotate_drivers = function(x,
#'                             drivers_list = CNAqc::DriverDBv3,
#'                             function_entries = c('exonic', "Exonic"),
#'                             function_column = 'ANNOVAR_FUNCTION',
#'                             gene_column = "GENE"
#' )
#' {
#'   stopifnot(inherits(x, 'cnaqc'))
#'
#'   cli::cli_alert_info("Looking for exonic mutations using column {gene_column} and {function_column}: entries will be {function_entries}.")
#'   if(!(gene_column %in% colnames(x$snvs))) stop("Gene column ", gene_column, " is not available in the data:\n\t", paste(colnames(x$snvs), collapse = ', '), '.')
#'   if(!(function_column %in% colnames(x$snvs))) stop("Function column ", function_column, " is not available in the data:\n\t", paste(colnames(x$snvs), collapse = ', '), '.')
#'
#'   to_find = x$snvs[[gene_column]][x$snvs[[function_column]] %in% function_entries] %>% sort %>% unique
#'
#'   cli::cli_alert_info("Found exonic mutations in {length(to_find)} genes")
#'   # print(to_find)
#'
#'   found = drivers_list %>%
#'     filter(driver_gene %in% to_find) %>%
#'     pull(driver_gene) %>%
#'     unique
#'
#'   cli::cli_alert_info("{length(found)} found in the input list of {length(drivers_list$driver_gene) %>% unique()} genes.")
#'   # if(length(found) > 0) print(found)
#'
#'   if(length(found) == 0) return(x)
#'
#'   which_driver = intersect(
#'     which(x$snvs[[gene_column]] %in% drivers_list$driver_gene),
#'     which(x$snvs[[function_column]] %in% function_entries)
#'   )
#'
#'   x$snvs$is_driver = FALSE
#'   x$snvs$is_driver[which_driver] = TRUE
#'
#'   cli::cli_h3('Drivers')
#'   x$snvs %>%
#'     filter(is_driver) %>%
#'     print
#'
#'   # cli::cli_alert_info("Reassembling a new CNAqc object with these drivers")
#'   # x = CNAqc::init(
#'   #   x$snvs,
#'   #   cna = x$cna,
#'   #   purity = x$purity,
#'   #   ref = x$reference_genome
#'   # )
#'
#'   # cli::cli_alert_info("Updating the CNAqc object with these drivers")
#'   return(x)
#' }
#'
#'
#' # exones_GRCh38
#'
#' # exones = exones_hg19
#' #
#' # exones_idxs = easypar::run(
#' #   FUN = function(i)
#' #   {
#' #     w = exones %>%
#' #       dplyr::filter(chr == x$snvs$chr[i],
#' #                     from <= x$snvs$from[i],
#' #                     to >= x$snvs$to[i]) %>%
#' #       distinct(gene)
#' #
#' #     if (nrow(w) > 0) {
#' #       # cli::cli_alert_success("Found exonic {.field {w$gene %>% paste(collapse = ':')}} mutation.")
#' #       return(data.frame(idx = i , ensemble_genes = paste(w$gene, collapse = ':')))
#' #     }
#' #     else
#' #       return(NULL)
#' #   },
#' #   PARAMS = lapply(1:nrow(x$snvs), list),
#' #   parallel = FALSE,
#' #   filter_errors = F,
#' #   export = 'exones'
#' # )
#' # exones_idxs = Reduce(bind_rows, exones_idxs)
#' #
#' # x$snvs$ensembl_exon = FALSE
#' # x$snvs$ensembl_exon[exones_idxs$idx] = TRUE
#' # x$snvs$ensembl_exon_gene = NA
#' # x$snvs$ensembl_exon_gene[exones_idxs$idx] = exones_idxs$ensemble_genes
#' #
#' # x$snvs %>% filter(ensembl_exon) %>% dplyr::select(GENE, ANNOVAR_FUNCTION, starts_with("ensembl_exon"))
#' #
#' # drv_list = CNAqc::DriverDBv3 %>%
#' #   distinct(driver_gene)
#' #
#' #   rename(ensembl_exon_gene = driver_gene)
#' #
#' # x$snvs = x$snvs %>%
#' #   left_join(drv_list, by = 'ensembl_exon_gene') %>%
#' #   mutate(is_driver = !is.na(n_tools))
#' #
#' # x$snvs %>% filter(is_driver) %>% dplyr::select(GENE, ANNOVAR_FUNCTION, starts_with("ensembl_exon"), cancer, n_tools) %>% View
#'
#'
#'
#' # exones_GRCh38 %>% filter(gene =='TP53') %>% pull(from) %>% min
#' # exones_GRCh38 %>% filter(gene =='TP53') %>% pull(from) %>% max
#' # gene_coordinates_GRCh38 %>% filter(gene =='TP53')