R/fqName.R

In ngsReports: Load FastqQC reports and other NGS related files

#' @title Return the Underlying Fastq File Names from FastqcData* Objects
#'
#' @description Return the Underlying Fastq File Names from FastqcData* Objects
#'
#' @param object An object of class FastqcData or FastqcDataList
#' @param value Replacement value for fqName
#'
#' @return Returns the names of the Fastq files the FastQC report was
#' generated from, without any preceding directories.
#'
#' @examples
#'
#' # Get the files included with the package
#' packageDir <- system.file("extdata", package = "ngsReports")
#' fl <- list.files(packageDir, pattern = "fastqc.zip", full.names = TRUE)
#'
#' # Load the FASTQC data as a FastqcDataList object
#' fdl <- FastqcDataList(fl)
#' fqName(fdl)
#'
#' @export
#' @rdname fqName-methods
setGeneric("fqName", function(object){standardGeneric("fqName")})
#' @export
#' @rdname fqName-methods
setMethod("fqName", "ANY", function(object){
    cl <- class(object)
    message("Method 'fqName' not implemented for objects of class ", cl)
})
#' @export
#' @name fqName
#' @aliases fqName,FastqcData-method
#' @rdname fqName-methods
setMethod("fqName", "FastqcData", function(object){
    object@Summary$Filename[1]
})
#' @export
#' @name fqName
#' @aliases fqName,FastqcDataList-method
#' @rdname fqName-methods
setMethod("fqName", "FastqcDataList", function(object){
    vapply(object@.Data, fqName, character(1))
})
#' @export
#' @rdname fqName-methods
setGeneric(
    "fqName<-", signature = "object",
    function(object, value) standardGeneric("fqName<-")
)
#' @export
#' @name fqName<-
#' @aliases fqName<-,FastqcData-method
#' @rdname fqName-methods
setReplaceMethod("fqName", signature = "FastqcData", function(object, value){
    stopifnot(length(value) == 1 | is.character(value))
    n <- nrow(object@Summary)
    object@Summary$Filename <- rep(value, n)
    object@Basic_Statistics$Filename <- value
    object
})
#' @export
#' @name fqName<-
#' @aliases fqName<-,FastqcDataList-method
#' @rdname fqName-methods
setReplaceMethod("fqName", signature = "FastqcDataList", function(object, value){
    stopifnot(length(value) == length(object))
    stopifnot(is.character(value))
    out <- lapply(
        seq_along(value),
        function(i, x = object){
            fqName(x[[i]]) <- value[i]
            x[[i]]
        }
    )
    as(out, "FastqcDataList")
})