R/get_exons.R

In Shians/NanoMethViz: Visualise methylation data from Oxford Nanopore sequencing

#' Get exon annotations
#'
#' Helper functions are provided for obtaining exon annotations from relevant
#' TxDb packages on Bioconductor for the construction of NanoMethResults
#' objects.
#'
#' @name get_exons
#' @rdname get_exons
#'
#' @return tibble (data.frame) object containing exon annotation.
#'
#' @importFrom tibble as_tibble
#' @importFrom dplyr rename
NULL

#' Get exon annotations for Mus musculus (mm10)
#'
#' @return data.frame containing exons
#'
#' @examples
#' m_musculus_exons <- get_exons_mus_musculus()
#'
#' @importFrom tibble as_tibble
#' @importFrom dplyr rename
#' @export
get_exons_mus_musculus <- function() {
    package_check("Mus.musculus", "1.3.1")

    genes <-  AnnotationDbi::keys(Mus.musculus::Mus.musculus, "GENEID")
    exon_data <- suppressMessages(AnnotationDbi::select(
        Mus.musculus::Mus.musculus,
        keys = genes,
        keytype = "GENEID",
        columns = c(
            "GENEID",
            "TXID",
            "EXONCHROM",
            "EXONSTRAND",
            "EXONSTART",
            "EXONEND",
            "SYMBOL"
        )
    ))

    tibble::as_tibble(exon_data) %>%
        dplyr::rename(
            gene_id = "GENEID",
            chr = "EXONCHROM",
            strand = "EXONSTRAND",
            start = "EXONSTART",
            end = "EXONEND",
            transcript_id = "TXID",
            symbol = "SYMBOL"
        )
}

#' @rdname get_exons
#'
#' @examples
#' mm10_exons <- get_exons_mm10()
#'
#' @export
get_exons_mm10 <- function() {
    package_check(
        c("TxDb.Mmusculus.UCSC.mm10.knownGene", "org.Mm.eg.db"),
        c("3.10.0", "3.15.0")
    )

    txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene::TxDb.Mmusculus.UCSC.mm10.knownGene

    genes <-  AnnotationDbi::keys(txdb, "GENEID")
    exon_data <- suppressMessages(AnnotationDbi::select(
        txdb,
        keys = genes,
        keytype = "GENEID",
        columns = c(
            "GENEID",
            "TXID",
            "EXONCHROM",
            "EXONSTRAND",
            "EXONSTART",
            "EXONEND"
        )
    ))

    symbols_data <- suppressMessages(AnnotationDbi::select(
            org.Mm.eg.db::org.Mm.eg.db,
            keys = genes,
            keytype = "ENTREZID",
            columns = c(
                "SYMBOL"
            )
        )) %>%
        dplyr::rename(GENEID = "ENTREZID")

    dplyr::left_join(exon_data, symbols_data, by = "GENEID", multiple = "all") %>%
        tibble::as_tibble() %>%
        dplyr::rename(
            gene_id = "GENEID",
            chr = "EXONCHROM",
            strand = "EXONSTRAND",
            start = "EXONSTART",
            end = "EXONEND",
            transcript_id = "TXID",
            symbol = "SYMBOL"
        )
}

#' @rdname get_exons
#'
#' @examples
#' grcm39_exons <- get_exons_grcm39()
#'
#' @export
get_exons_grcm39 <- function() {
    package_check(
        c("TxDb.Mmusculus.UCSC.mm39.refGene", "org.Mm.eg.db"),
        c("3.10.0", "3.15.0")
    )

    txdb <- TxDb.Mmusculus.UCSC.mm39.refGene::TxDb.Mmusculus.UCSC.mm39.refGene

    genes <-  AnnotationDbi::keys(txdb, "GENEID")
    exon_data <- suppressMessages(AnnotationDbi::select(
        txdb,
        keys = genes,
        keytype = "GENEID",
        columns = c(
            "GENEID",
            "TXID",
            "EXONCHROM",
            "EXONSTRAND",
            "EXONSTART",
            "EXONEND"
        )
    ))

    symbols_data <- suppressMessages(AnnotationDbi::select(
            org.Mm.eg.db::org.Mm.eg.db,
            keys = genes,
            keytype = "ENTREZID",
            columns = c(
                "SYMBOL"
            )
        )) %>%
        dplyr::rename(GENEID = "ENTREZID")

    dplyr::left_join(exon_data, symbols_data, by = "GENEID", multiple = "all") %>%
        tibble::as_tibble() %>%
        dplyr::rename(
            gene_id = "GENEID",
            chr = "EXONCHROM",
            strand = "EXONSTRAND",
            start = "EXONSTART",
            end = "EXONEND",
            transcript_id = "TXID",
            symbol = "SYMBOL"
        )
}

#' Get example exon annotations for mus musculus (mm10)
#'
#' This is a small subset of the exons returned by
#' \code{get_exons_mus_musculus()} for demonstrative purposes. It contains
#' the exons for the genes Brca1, Brca2, Impact, Meg3, Peg3 and Xist.
#'
#' @return data.frame containing exons
#'
#' @examples
#' example_exons <- get_example_exons_mus_musculus()
#'
#' @export
get_example_exons_mus_musculus <- function() {
    package_check("Mus.musculus", "1.3.1")

    genes <-  c("12189", "12190", "16210", "17263", "18616", "213742")
    exon_data <- suppressMessages(AnnotationDbi::select(
        Mus.musculus::Mus.musculus,
        keys = genes,
        keytype = "GENEID",
        columns = c(
            "GENEID",
            "TXID",
            "EXONCHROM",
            "EXONSTRAND",
            "EXONSTART",
            "EXONEND",
            "SYMBOL"
        )
    ))

    tibble::as_tibble(exon_data) %>%
        dplyr::rename(
            gene_id = "GENEID",
            chr = "EXONCHROM",
            strand = "EXONSTRAND",
            start = "EXONSTART",
            end = "EXONEND",
            transcript_id = "TXID",
            symbol = "SYMBOL"
        )
}

#' Get exon annotations for Homo sapiens (hg19)
#'
#' @return data.frame containing exons
#'
#' @examples
#' h_sapiens_exons <- get_exons_homo_sapiens()
#'
#' @importFrom tibble as_tibble
#' @importFrom dplyr rename
#' @export
get_exons_homo_sapiens <- function() {
    package_check("Homo.sapiens", "1.3.1")

    genes <-  AnnotationDbi::keys(Homo.sapiens::Homo.sapiens, "GENEID")
    exon_data <- suppressMessages(AnnotationDbi::select(
        Homo.sapiens::Homo.sapiens,
        keys = genes,
        keytype = "GENEID",
        columns = c(
            "GENEID",
            "TXID",
            "EXONCHROM",
            "EXONSTRAND",
            "EXONSTART",
            "EXONEND",
            "SYMBOL"
        )
    ))

    tibble::as_tibble(exon_data) %>%
        dplyr::rename(
            gene_id = "GENEID",
            chr = "EXONCHROM",
            strand = "EXONSTRAND",
            start = "EXONSTART",
            end = "EXONEND",
            transcript_id = "TXID",
            symbol = "SYMBOL"
        )

}

#' @rdname get_exons
#'
#' @examples
#' hg19_exons <- get_exons_hg19()
#'
#' @export
get_exons_hg19 <- function() {
    package_check(
        c("org.Hs.eg.db", "TxDb.Hsapiens.UCSC.hg19.knownGene"),
        c("3.15.0", "3.2.2"))

    txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene
    genes <-  AnnotationDbi::keys(txdb, "GENEID")
    exon_data <- suppressMessages(AnnotationDbi::select(
        txdb,
        keys = genes,
        keytype = "GENEID",
        columns = c(
            "GENEID",
            "TXID",
            "EXONCHROM",
            "EXONSTRAND",
            "EXONSTART",
            "EXONEND"
        )
    ))

    symbols_data <- suppressMessages(AnnotationDbi::select(
            org.Hs.eg.db::org.Hs.eg.db,
            keys = genes,
            keytype = "ENTREZID",
            columns = c(
                "SYMBOL"
            )
        )) %>%
        dplyr::rename(GENEID = "ENTREZID")

    dplyr::left_join(exon_data, symbols_data, by = "GENEID", multiple = "all") %>%
        tibble::as_tibble() %>%
        dplyr::rename(
            gene_id = "GENEID",
            chr = "EXONCHROM",
            strand = "EXONSTRAND",
            start = "EXONSTART",
            end = "EXONEND",
            transcript_id = "TXID",
            symbol = "SYMBOL"
        )
}

#' @rdname get_exons
#'
#' @examples
#' hg38_exons <- get_exons_hg38()
#'
#' @export
get_exons_hg38 <- function() {
    package_check(
        c("org.Hs.eg.db", "TxDb.Hsapiens.UCSC.hg38.knownGene"),
        c("3.15.0", "3.15.0"))

    txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene::TxDb.Hsapiens.UCSC.hg38.knownGene
    genes <-  AnnotationDbi::keys(txdb, "GENEID")
    exon_data <- suppressMessages(AnnotationDbi::select(
        txdb,
        keys = genes,
        keytype = "GENEID",
        columns = c(
            "GENEID",
            "TXID",
            "EXONCHROM",
            "EXONSTRAND",
            "EXONSTART",
            "EXONEND"
        )
    ))

    symbols_data <- suppressMessages(AnnotationDbi::select(
            org.Hs.eg.db::org.Hs.eg.db,
            keys = genes,
            keytype = "ENTREZID",
            columns = c(
                "SYMBOL"
            )
        )) %>%
        dplyr::rename(GENEID = "ENTREZID")

    dplyr::left_join(exon_data, symbols_data, by = "GENEID", multiple = "all") %>%
        tibble::as_tibble() %>%
        dplyr::rename(
            gene_id = "GENEID",
            chr = "EXONCHROM",
            strand = "EXONSTRAND",
            start = "EXONSTART",
            end = "EXONEND",
            transcript_id = "TXID",
            symbol = "SYMBOL"
        )
}

#' @importFrom utils installed.packages packageVersion
package_check <- function(packages, req_versions) {
    assertthat::assert_that(length(packages) == length(req_versions))

    any_missing <- FALSE
    for (i in seq_along(packages)) {
        package <- packages[i]
        req_version <- req_versions[i]
        if (package %in% utils::installed.packages()) {
            if (packageVersion(package) < req_version) {
                any_missing <- TRUE
                message(glue::glue(
                    "required package '{package} (>= {req_version})' is not installed, please install using BiocManager::install({package})"
                ))
             }
        }
    }

    if (any_missing) {
        stop("please install required packages before continuing")
    }
}