shmootl: QTL Analysis Utilities for Yeast

#' @section Chromosomes and Sequences:
#' 
#' Although for some yeast genome assemblies they are equivalent, chromosomes
#' (cell structures containing genetic material) are treated by \pkg{shmootl}
#' as being distinct from sequences (linkage units that corresponding to all
#' or part of a chromosome). This distinction is necessary to allow for use of
#' reference genomes in which multiple sequences map to a single chromosome.
#' (see \code{\link{genomeOpt}} for more on setting a reference genome.) While
#' every sequence must be mapped to a specific chromosome, it is sequences,
#' and not chromosomes, that are used as the primary linkage unit throughout
#' this package.
#' 
#' \subsection{Chromosomes}{
#' A yeast nuclear chromosome can be represented by an Arabic number in the
#' range \code{1} to \code{16}, inclusive; or by the Roman numeral corresponding
#' to the chromosome number. The mitochondrial chromosome can be represented by
#' the number \code{17} or a capital \code{'M'}. A chromosome label can include
#' one of the optional prefixes \code{'c'} or \code{'chr'}. So for example, any
#' of the following can represent chromosome 4:
#' 
#' \itemize{
#' \item{\code{4}:}{an Arabic number}
#' \item{\code{IV}:}{a Roman numeral}
#' \item{\code{c04}:}{a zero-padded Arabic number with prefix \code{'c'}}
#' \item{\code{chrIV}:}{a Roman numeral with prefix \code{'chr'}}
#' }
#' 
#' Using the function \code{\link{normChr}}, all of these representations can
#' be normalised to one consistent form: a zero-padded Arabic number
#' (i.e. \code{'04'}). This is used internally by \pkg{shmootl} as a
#' normalised representation, and is recommended.
#' }
#' 
#' \subsection{Sequences}{
#' For genomes in which every sequence represents a specific chromosome, the
#' sequence label is identical to the chromosome label. In other cases, the
#' sequence label should be a chromosome label followed by a sequence-specific
#' label (e.g. contig ID), separated by an underscore. For example, a contig
#' \code{'1D22'} that maps to chromosome 4 can be represented as follows:
#' 
#' \itemize{
#' \item{\code{4_1D22}}
#' \item{\code{IV_1D22}}
#' \item{\code{c04_1D22}}
#' \item{\code{chrIV_1D22}}
#' }
#' 
#' Variations in chromosome representation are possible as before, but the
#' sequence-specific label must be consistent. As with chromosomes, the function
#' \code{\link{normSeq}} can be used to normalise all of these forms to
#' one consistent representation: a zero-padded Arabic number followed by the
#' sequence-specific label (i.e. \code{'04_1D22'}). This representation is
#' recommended, as it is used internally by \pkg{shmootl} as a standard way to
#' label sequences in a genome lacking a one-to-one correspondence between
#' sequences and chromosomes.
#' }