R/markposDFs.R

In idiogramFISH: Shiny App. Idiograms with Marks and Karyotype Indices

#' @title Mark Positional data - monocentrics
#' @description When several OTUs, some can be monocen. and others holocen.
#' Marks distance for
#' monocen. are measured from cen. and for
#' holocen. from top or bottom depending on \code{param} \code{origin}. See
#' vignettes.
#'
#' @docType data
#' @name markposDFs
NULL
#' @description bigdfOfMarks: Example data for mark position with column OTU
#'
#' @format bigdfOfMarks a data.frame with columns:
#' \describe{
#'   \item{OTU}{OTU, species, mandatory if in dfChrSize}
#'   \item{chrName}{name of chromosome}
#'   \item{markName}{name of mark}
#'   \item{chrRegion}{use p for short arm, q for long arm, and cen for
#' centromeric}
#'   \item{markDistCen}{distance of mark to centromere (not for cen)}
#'   \item{markSize}{size of mark (not for cen)}
#' }
#' @seealso \code{\link{markdataholo}}
#' @seealso \code{\link{plotIdiograms}}
#' @seealso \code{\link{chrbasicdatamono}}
#' @seealso \code{\link{dfMarkColor}}
#'
#' @rdname markposDFs
"bigdfOfMarks"
#' @description dfOfMarks: Example data for marks' position
#' @rdname markposDFs
"dfOfMarks"
#' @description dfOfMarks2: Marks' position including cen. marks
#' @rdname markposDFs
"dfOfMarks2"
#' @description humMarkPos: human karyotype bands' (marks) positions, measured
#' from Adler (1994)
#' @source
#' \href{http://www.pathology.washington.edu/research/cytopages/idiograms/human/}{Washington U}
#' @references Adler 1994. Idiogram Album. URL:
#' \href{http://www.pathology.washington.edu/research/cytopages/idiograms/human/}{Washington U.}
#' @rdname markposDFs
"humMarkPos"
#' @description allMarksSample: Example data for marks' position
#' @rdname markposDFs
"allMarksSample"
#' @description dfAlloParentMarks: Example data for mark position of GISH of
#' monocen.
#' @rdname markposDFs
"dfAlloParentMarks"
#' @description traspaMarks: T. spathacea (Rhoeo) marks' positions, from
#' Golczyk et al. (2005)
#' @references Golczyk H, Hasterok R, Joachimiak AJ (2005) FISH-aimed
#' karyotyping and
#' characterization of Renner complexes in permanent heterozygote Rhoeo
#' spathacea. Genome
#' 48:145-153.
#' @rdname markposDFs
"traspaMarks"