#' 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() || 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")
}
}
