R/arrange.R

In lgatto/tidyms: A Grammar of Data Manipulation for Omics Experiments

##' @export
##' @rdname tidies
##' @param .data An object of class [MSnbase::MSnSet].
##' @param ...  Expressions evaluated in the context of the object's
##'     feature and sample variable and passed to the `dplyr`
##'     functions. Ignored in `as_tibble,MSnSet`.
##' @md
arrange.eSet <- function(.data, ...) {
    fd <- fData(.data)
    fd$.__featureNames__ <- featureNames(.data)
    fd <- try(arrange(fd, ...), silent = TRUE)
    pd <- pData(.data)
    pd$.__sampleNames__ <- sampleNames(.data)
    pd <- try(arrange(pd, ...), silent = TRUE)
    if (!inherits(fd, "try-error")) {
        .data <- .data[fd$.__featureNames_, ]
        rownames(fd) <- fd$.__featureNames__
        fd$.__featureNames__ <- NULL
        fData(.data) <- fd
    } else if (!inherits(pd, "try-error")) {
        .data <- .data[, pd$.__sampleNames__]
        rownames(pd) <- pd$.__sampleNames__
        pd$.__sampleNames__ <- NULL
        pData(.data) <- pd
    }
    .data
}