R/TheoreticalGC.R

In UofABioinformaticsHub/fastqcReports: Load FastqQC reports and other NGS related files

#' @title The TheoreticalGC Object Class
#'
#' @description Contains Theoretical GC content for a selection of species
#'
#' @details Estimates are able to be retained for genomic and transcriptomic
#' sequences. Values are stored as frequencies.
#'
#' @return An object of class TheoreticalGC
#'
#' @include validationFunctions.R
#'
#' @slot Genome A `data.frame` containing theoretical GC content for
#' genomic sequences
#' @slot Transcriptome A `data.frame` containing theoretical GC content
#' for transcriptomic sequences
#' @slot mData A `data.frame` containing metadata about all species in the
#' object
#'
#' @examples
#'
#' ## How to form an object using your own fasta file
#' faDir <- system.file("extdata", package = "ngsReports")
#' faFile <- list.files(faDir, pattern = "fasta", full.names = TRUE)
#' gen_df <- estGcDistn(faFile, n = 200)
#' gen_df <- dplyr::rename(gen_df, Athaliana = Freq)
#' mData_df <-
#'     data.frame(Name = "Athaliana", Genome = TRUE, Transcriptome = FALSE)
#' tr_df <- data.frame()
#' myGC <- new(
#'    "TheoreticalGC", Genome = gen_df, Transcriptome = tr_df, mData = mData_df)
#'
setClass("TheoreticalGC",  slots = c(
    Genome = "data.frame",
    Transcriptome = "data.frame",
    mData = "data.frame")
)
setValidity("TheoreticalGC", .isValidTheoreticalGC)

#' @title Extract Metadata for TheoreticalGC objects
#'
#' @description Extract Metadata for TheoreticalGC objects
#'
#' @param object An object of class Theoretical GC
#'
#' @return A `tibble` object
#'
#' @examples
#' mData(gcTheoretical)
#'
#' @export
#' @name mData
#' @rdname mData
setGeneric("mData", function(object) standardGeneric("mData"))

#' @importFrom methods slot
#' @export
#' @rdname mData
#' @aliases mData,TheoreticalGC-method
setMethod("mData", "TheoreticalGC", function(object){object@mData})

#' @title List Genomes or Transcriptomes with Theoretical GC Content
#'
#' @description
#' List available genomes or transcriptomes in a TheoreticalGC object
#'
#' @details
#' An object of class TheoreticalGC can hold the theoretical GC content for one
#' or more species, for either the genome or transriptome.
#' This function checks which species are available in the given object, for
#' either the genome or transcriptome, as supplied to the parameter `type`.
#'
#' @param object An object of class TheoreticalGC
#' @param type character indicating either Genome or Transcriptome
#'
#' @return A `tibble` object
#'
#' @examples
#' gcAvail(gcTheoretical, "Genome")
#'
#' @export
setGeneric("gcAvail", function(object, type) standardGeneric("gcAvail"))


#' @importFrom methods slot
#' @importFrom tidyselect ends_with
#' @importFrom stringr str_to_title
#' @export
#' @rdname gcAvail
#' @aliases gcAvail,TheoreticalGC-method
setMethod("gcAvail", "TheoreticalGC", function(object, type){

        type <- match.arg(str_to_title(type), c("Genome", "Transcriptome"))
        ln <- slot(object, "mData")[[type]]
        df <- slot(object, "mData")[ln,]
        dplyr::select(df, -ends_with("ome"))
    })

setMethod("show", "TheoreticalGC", function(object){
    meta <- mData(object)
    nGenomes <- sum(meta$Genome)
    nTranscriptomes <- sum(meta$Transcriptome)
    cat("TheoreticalGC Object for:\n")
    cat(nGenomes, "Genomes &", nTranscriptomes, "Transcriptomes\n")
})