R/examples.R

In teunbrand/ggnomics: ggnomics

#' Example gene models
#'
#' Generates a \code{GRanges} compatible with \code{geom_genemodel}.
#'
#' @return A \code{GRanges} object of length 165.
#' @export
#'
#' @details The result contains about one megabase's worth of genes on human
#'   chromosome 17. Data was taken from GRCh38.92 (hg38) gene models from
#'   \href{https://www.ensembl.org/}{Ensembl} and was edited to somewhat
#'   simplify data. Original \code{.gtf} file is available at the
#'   \href{ftp://ftp.ensembl.org/pub/release-97/gtf/homo_sapiens/}{Ensembl
#'   database}.
#'
#' @seealso \code{\link[ggnomics]{geom_genemodel}}
#'
#' @examples
#' gm <- example_genemodels()
#' print(gm)
example_genemodels <- function() {
    GenomicRanges::GRanges(
        seqnames = "chr17",
        ranges = IRanges::IRanges(
            start = c(63728411L, 63751940L, 63702845L, 63706635L, 63710728L,
                      63713406L, 63723298L, 63726638L, 63484868L, 63493436L,
                      63507056L, 63484823L, 63507629L, 63513382L, 63518928L,
                      63477095L, 63493436L, 63477061L, 63484840L, 63479859L,
                      63493436L, 63746884L, 63751871L, 63760914L, 63764016L,
                      63756311L, 63760914L, 63764016L, 63772777L, 63745250L,
                      63751770L, 63929229L, 63932262L, 63928740L, 63895025L,
                      63895755L, 63894909L, 63872129L, 63872859L, 63872012L,
                      63909714L, 63918767L, 63910444L, 63918777L, 63909597L,
                      63433349L, 63437461L, 63445898L, 63432304L, 63550678L,
                      63578470L, 63583502L, 63589000L, 63550461L, 63589173L,
                      63787050L, 63792412L, 63798038L, 63805044L, 63815563L,
                      63773603L, 63787034L, 63792412L, 63800470L, 63805059L,
                      63818068L, 63819805L, 63826903L, 63819433L, 63825343L,
                      63917312L, 63918777L, 63917200L, 63880236L, 63881802L,
                      63880215L, 63523414L, 63530091L, 63533886L, 63542241L,
                      63523334L, 63530115L, 63533886L, 63542241L, 63548802L,
                      63698555L, 63698876L, 63695902L, 63622760L, 63632681L,
                      63646034L, 63652557L, 63657794L, 63666940L, 63681766L,
                      63685517L, 63688527L, 63622415L, 63652565L, 63657794L,
                      63666940L, 63672845L, 63681766L, 63685517L, 63688527L,
                      63998365L, 63998351L, 63827491L, 63827152L, 63829915L,
                      63940774L, 63957162L, 63963672L, 63971162L, 63972842L,
                      63938554L, 63832941L, 63842459L, 63837617L, 63842381L,
                      63832081L, 63703602L, 63710491L, 63713406L, 63717075L,
                      63723298L, 63726638L, 63713424L, 63717093L, 63726638L,
                      63737396L, 63741168L, 63682336L, 63689093L, 63702819L,
                      63710491L, 63713406L, 63717075L, 63601084L, 63604534L,
                      63600872L, 63608003L, 63009560L, 63073943L, 63099175L,
                      63151270L, 63193991L, 63200771L, 63237814L, 63267748L,
                      63314388L, 63318957L, 63340101L, 63351250L, 63354783L,
                      63379718L, 63388635L, 63395743L, 63398821L, 63405122L,
                      63411511L, 63418307L, 63009556L, 63399043L, 63420062L),
            end   = c(63728413L, 63752097L, 63704582L, 63707418L, 63710836L,
                      63714108L, 63723326L, 63728407L, 63491381L, 63496985L,
                      63507625L, 63484867L, 63510832L, 63514094L, 63521848L,
                      63491381L, 63497363L, 63477541L, 63484867L, 63491381L,
                      63498380L, 63746961L, 63756570L, 63761351L, 63766175L,
                      63756570L, 63761351L, 63766194L, 63776351L, 63746880L,
                      63751867L, 63932261L, 63932354L, 63929225L, 63896511L,
                      63896661L, 63895157L, 63873614L, 63873766L, 63872528L,
                      63911196L, 63918776L, 63911341L, 63918838L, 63909846L,
                      63440199L, 63442852L, 63446378L, 63435110L, 63550815L,
                      63579943L, 63585328L, 63589169L, 63550677L, 63594266L,
                      63787270L, 63792562L, 63800617L, 63813454L, 63818395L,
                      63775178L, 63787049L, 63792547L, 63800617L, 63813290L,
                      63819317L, 63826902L, 63827671L, 63821828L, 63826642L,
                      63918776L, 63918838L, 63917423L, 63881801L, 63881935L,
                      63880456L, 63524369L, 63530542L, 63538662L, 63545899L,
                      63523413L, 63530542L, 63538662L, 63546727L, 63548977L,
                      63699298L, 63701172L, 63698551L, 63622763L, 63634801L,
                      63646074L, 63652656L, 63657907L, 63668162L, 63681899L,
                      63685590L, 63693774L, 63622759L, 63652656L, 63657907L,
                      63668334L, 63672914L, 63681899L, 63685590L, 63696303L,
                      63999074L, 63998984L, 63831966L, 63828137L, 63832026L,
                      63951900L, 63961431L, 63968355L, 63972841L, 63972918L,
                      63940770L, 63838681L, 63842674L, 63838728L, 63843065L,
                      63837210L, 63707418L, 63710836L, 63714108L, 63717154L,
                      63723326L, 63728369L, 63714108L, 63717154L, 63728413L,
                      63737436L, 63741986L, 63682758L, 63690597L, 63707510L,
                      63710836L, 63714108L, 63717125L, 63601363L, 63607999L,
                      63601083L, 63608365L, 63009626L, 63074014L, 63099357L,
                      63151380L, 63194139L, 63200957L, 63238077L, 63267873L,
                      63314669L, 63319090L, 63340332L, 63351416L, 63355390L,
                      63379826L, 63389544L, 63395928L, 63399039L, 63406277L,
                      63415674L, 63421952L, 63009559L, 63399286L, 63427699L)
        ),
        strand = Rle(
            values = factor(
                rep(c("-", "+"), 5),
                levels = c("+", "-", "*")
            ),
            lengths = c(8, 13, 28, 17, 10, 9, 3, 22, 28, 27)
        ),
        type = factor(rep(c(1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L,
                            2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L,
                            1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L,
                            2L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L),
                          c(2L, 6L, 3L, 4L, 2L, 4L, 4L, 6L, 1L, 2L, 1L, 2L, 1L,
                            2L, 2L, 3L, 1L, 3L, 4L, 2L, 5L, 6L, 1L, 3L, 1L, 2L,
                            1L, 2L, 4L, 5L, 1L, 2L, 9L, 8L, 1L, 1L, 1L, 2L, 4L,
                            2L, 2L, 3L, 6L, 11L, 2L, 2L, 20L, 3L)),
                      labels = c("CDS", "UTR")),
        name = rep(c("AC046185.1", "AC113554.1", "ACE", "CCDC47", "CD79B",
                     "CSH1", "CSH2", "CSHL1", "CYB561", "DCAF7", "DDX42",
                     "FTSJ3", "GH1", "GH2", "KCNH6", "LIMD2", "MAP3K3", "PRR29",
                     "PSMC5", "SCN4A", "SMARCD2", "STRADA", "TACO1", "TANC2"),
                   c(8L, 7L, 6L, 10L, 3L, 3L, 3L, 5L, 4L, 6L, 11L, 4L, 3L, 3L, 9L,
                     3L, 17L, 2L, 3L, 6L, 5L, 17L, 4L, 23L)),
        seqinfo = GenomeInfoDb::Seqinfo("chr17", 83257441L, FALSE,
                                        genome = "hg38")
    )
}