man-roxygen/BiomartGeneRegionTrack-class_param.R

In ivanek/Gviz: Plotting data and annotation information along genomic coordinates

#' @param x A valid track object class name, or the object itself, in which
#' case the class is derived directly from it.
#' @param use.defaults `logical`
#' @param filter filter
#' @param range range
#' @param from,to from, to
#' @param .Object .Object
#'
#' @param start An integer scalar with the genomic start coordinates for the
#' gene model range.
#' @param end An integer scalar with the genomic end coordinates for the gene
#' model range.
#' @param biomart An optional \code{\linkS4class{Mart}} object providing access
#' to the EBI Biomart webservice. As default the appropriate Ensembl data
#' source is selected based on the provided genome and chromosome.
#' @param strand Character scalar, the strand for which to fetch gene
#' information from Biomart. One in \code{+}, \code{-}, or \code{+-}.
#' @param chromosome The chromosome on which the track's genomic ranges are
#' defined. A valid UCSC chromosome identifier. Please note that at this stage
#' only syntactic checking takes place, i.e., the argument value needs to be a
#' single integer, numeric character or a character of the form \code{chrx},
#' where \code{x} may be any possible string. The user has to make sure that
#' the respective chromosome is indeed defined for the the track's genome.
#' @param genome The genome on which the track's ranges are defined. Usually
#' this is a valid UCSC genome identifier, however this is not being formally
#' checked at this point. If no mapping from genome to Biomart Ensembl data
#' source is possible, the \code{biomart} argument needs to be provided by the
#' user.
#' @param stacking The stacking type for overlapping items of the track. One in
#' \code{c(hide, dense, squish, pack,full)}. Currently, only hide (don't show
#' the track items, squish (make best use of the available space) and dense (no
#' stacking at all) are implemented.
#' @param filters A list of additional filters to be applied in the Biomart
#' query. See \code{\link{getBM}} for details.
#' @param featureMap Named character vector or list to map between the fields
#' in the Biomart data base and the features as they are used to construct the
#' track. If multiple values are provided in a single list item, the package
#' will use the first one that is defined in the selected Biomart.
#' @param name Character scalar of the track's name used in the title panel
#' when plotting.
#' @param symbol,transcript,gene,entrez Character vector giving one or several
#' gene symbols, Ensembl transcript identifiers, Ensembl gene identifiers, or
#' ENTREZ gene identifiers, respectively. The genomic locus of their gene model
#' will be fetch from Biomart instead of providing explicit start and end
#' coordinates.
#' @param \dots Additional items which will all be interpreted as further
#' display parameters. See \code{\link{settings}} and the "Display Parameters"
#' section below for details.