R/get_genome_annotation.R

In ShixiangWang/sigminer: Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

#' Get Genome Annotation
#'
#' @param data_type 'chr_size' for chromosome size,
#' 'centro_loc' for location of centromeres,
#' 'cytobands' for location of chromosome cytobands
#' and 'transcript' for location of transcripts.
#' @param genome_build one of 'hg19', 'hg38'
#' @param chrs chromosomes start with 'chr'
#' @return a `data.frame` containing annotation data
#' @examples
#' df1 <- get_genome_annotation()
#' df1
#'
#' df2 <- get_genome_annotation(genome_build = "hg38")
#' df2
#'
#' df3 <- get_genome_annotation(data_type = "centro_loc")
#' df3
#'
#' df4 <- get_genome_annotation(data_type = "centro_loc", genome_build = "hg38")
#' df4
#'
#' df5 <- get_genome_annotation(data_type = "cytobands")
#' df5
#'
#' df6 <- get_genome_annotation(data_type = "cytobands", genome_build = "hg38")
#' df6
#' @testexamples
#' expect_equal(nrow(df1), nrow(df2))
#' expect_equal(nrow(df3), nrow(df4))
#' expect_equal(nrow(df5), nrow(df6))
#'
#' expect_equal(identical(df1, df2), FALSE)
#' expect_equal(identical(df3, df4), FALSE)
#' expect_equal(identical(df5, df6), FALSE)
#' @export
get_genome_annotation <- function(data_type = c("chr_size", "centro_loc", "cytobands", "transcript", "gene"),
                                  chrs = paste0("chr", c(1:22, "X", "Y")),
                                  genome_build = c("hg19", "hg38", "T2T", "mm10", "mm9", "ce11")) {
  data_type <- match.arg(data_type)
  genome_build <- match.arg(genome_build)

  prefix <- switch(data_type,
                   chr_size = "chromsize",
                   centro_loc = "centromeres",
                   cytobands = "cytobands",
                   transcript = "transcript",
                   gene = "gene"
  )

  if (prefix == "gene") {
    gene_file <- switch(
      genome_build,
      mm9 = file.path(
        system.file("extdata", package = "sigminer"),
        "mouse_mm9_gene_info.rds"
      ),
      mm10 = file.path(
        system.file("extdata", package = "sigminer"),
        "mouse_mm10_gene_info.rds"
      ),
      ce11 = file.path(
        system.file("extdata", package = "sigminer"),
        "ce11_gene_info.rds"
      ),
      file.path(
        system.file("extdata", package = "sigminer"),
        paste0("human_", genome_build, "_gene_info.rds")
      )
    )
    ok <- TRUE
    if (!file.exists(gene_file)) ok <- query_remote_data(basename(gene_file))
    if (!ok) {
      return(invisible(NULL))
    }
    annot <- readRDS(gene_file)
  } else {
    annot <- get(paste(prefix, genome_build, sep = "."), envir = tryCatch(
      as.environment("package:sigminer"),
      error = function(e) {
        eval(parse(text = "attachNamespace('sigminer')"))
        as.environment("package:sigminer")
      }
    ))
  }

  res <- annot %>%
    dplyr::filter(.data$chrom %in% chrs) %>%
    dplyr::arrange(factor(.data$chrom, chrs))

  res
}