R/functions-EnsDb.R

In jotsetung/ensembldb: Utilities to create and use Ensembl-based annotation databases

## Functions related to EnsDb objects.

#' @title Globally filter an EnsDb database
#'
#' @description \code{.addFilter} globally filters the provided
#'     \code{EnsDb} database, i.e. it returns a \code{EnsDb} object with the
#'     provided filter permanently set and active.
#'
#' @details Adding a filter to an \code{EnsDb} object causes this filter to be
#'     permanently active. The filter will be used for all queries to the
#'     databases and is added to all additional filters passed to the methods.
#'
#' @param x An \code{EnsDb} object on which the filter(s) should be set.
#'
#' @param filter An \code{\link[AnnotationFilter]{AnnotationFilterList}},
#'     \code{\link[AnnotationFulter]{AnnotationFilter}} object or a filter
#'     expression providing the filter(s) to be set.
#'
#' @return For \code{.addFilter}: the \code{EnsDb} object with the filter
#'     globally added and enabled.
#'
#'     For \code{.dropFilter}: the \code{EnsDb} object with all filters removed.
#'
#'     For \code{.activeFilter}: an \code{}
#'
#' @author Johannes Rainer
#'
#' @noRd
.addFilter <- function(x, filter = AnnotationFilterList()) {
    if (length(filter) == 0)
        stop("No filter provided")
    filter <- .processFilterParam(filter, x)
    ## Now, if there was no error, filter is an AnnotationFilterList
    got_filter <- getProperty(x, "FILTER")
    if (is(got_filter, "AnnotationFilter") |
        is(got_filter, "AnnotationFilterList")) {
        ## Append the new filter.
        filter <- AnnotationFilterList(got_filter, filter)
    } else {
        if (!is.na(got_filter))
            stop("Globally set filter is not an 'AnnotationFilter' or ",
                 "'AnnotationFilterList'")
    }
    x@.properties$FILTER <- filter
    x
}

#' @description \code{.dropFilter} drops all (globally) added filters from the
#'     submitted \code{EnsDb} object.
#'
#' @noRd
.dropFilter <- function(x) {
    dropProperty(x, "FILTER")
}

#' @description \code{.activeFilter} lists the globally set and active filter(s)
#'     of an \code{EnsDb} object.
#'
#' @noRd
.activeFilter <- function(x) {
    getProperty(x, "FILTER")
}


#' @aliases filter
#'
#' @description \code{filter} filters an \code{EnsDb} object. \code{filter} is
#'     an alias for the \code{addFilter} function.
#'
#' @rdname global-filters
filter <- function(x, filter = AnnotationFilterList()) {
    if (is(x, "EnsDb"))
        addFilter(x, filter)
    else
        stop("ensembldb::filter requires an 'EnsDb' object as input. To call ",
             "the filter function from the stats or dplyr package use ",
             "stats::filter and dplyr::filter instead.")
}

.has_tx_external_name <- function(x) {
    any(listTables(x)$tx == "tx_external_name")
}

#' Fix for the incorrect/failing is_circular information from Ensembl. If the
#' chromosome matches a certain pattern replace it with `TRUE`, otherwise use
#' the info from the chromosome table.
#'
#' @param x `data.frame` with a column `"seq_name"` and one `"is_circular"`.
#'
#' @param mt_pattern `character` defining chromosome names expected to be
#'     circular.
#'
#' @return `data.frame` with the *fixed* is_circular information.
#' @noRd
.fix_is_circular <- function(x, mt_pattern = "MT") {
    x$is_circular[x$seq_name %in% mt_pattern] <- 1
    x
}