R/data.R

In ngsReports: Load FastqQC reports and other NGS related files

#' @title Theoretical GC content
#'
#' @description This object contains the theoretical GC content for each
#' provided species, for both the genome and transcriptome, where available.
#'
#' @details The object is defined with the S4 class \code{TheoreticalGC}.
#' Species for which information is available can be found using
#' the command \code{gcAvail(gcTheoretical)} and selecting the appropriate type.
#'
#' Metadata is accessible using \code{mData(gcTheoretical)}.
#'
#' All GC content was calculated using code from
#' https://github.com/mikelove/fastqcTheoreticalGC using BSgenome packages.
#' This provides a default set of GC content data for common organisms
#' generated using 100bp reads/fragments and 1e6 reads.
#'
#' @seealso gcAvail
#'
#' @examples
#' ## Check which genomes are included
#' gcAvail(gcTheoretical, "Genome")
#'
#' ## Check which transcriptomes are included
#' gcAvail(gcTheoretical, "Transcriptome")
#'
#'
"gcTheoretical"