#' Automatic Feature Id Conversion.

#'

#' Attempt to automatically convert non-ENSEMBL feature identifiers to

#' ENSEMBL identifiers. Features are included as rownames of the input

#' data.frame (or matrix). It is assumed that feature identifiers

#' (i.e., rownames of x) come from human or mouse genomes, and

#' are either OFFICIAL SYMBOLS or ENTREZIDS. If less than 20% of match

#' is identified, an error will be thrown.

#'

#' @param x data.frame or matrix including raw counts (typically, UMIs),

#'   where rows are features (genes) and rownames are feature identifiers

#'   (SYMBOLs or ENTREZIDs).

#' @param verbose logical, shall messages be printed to inform about

#'   conversion advances.

#'

#' @return a data.frame where rownames are ENSEMBL IDs. The new feature IDs are

#' automatically imputed based on existing feature IDs (SYMBOLs or ENTREZIDs).

#'

#' @export

customConvertFeats <- function(x, verbose = TRUE) {

  if (!(is.matrix(x) || is.data.frame(x))) {

    stop("wrong input")

  }

  # uncomment

  myDict <- DIscBIO::HumanMouseGeneIds

  myDict <- myDict[!is.na(myDict[, "ENSEMBL"]), ]

  #

  xx <- rownames(x)

  keep.ei <- xx %in% myDict[, "ENTREZID"]

  keep.sy <- xx %in% myDict[, "SYMBOL"]

  keep.ez <- xx %in% myDict[, "ENSEMBL"]

  rat.ez <- sum(keep.ez) / length(xx)

  rat.ei <- sum(keep.ei) / length(xx)

  rat.sy <- sum(keep.sy) / length(xx)

  # Automatic selection and replacement

  if (rat.ez >= rat.sy && rat.ez >= rat.ei && rat.ez >= 0.2) {

    # nothing to do, return

    return(x)

  } else if (rat.ei >= rat.sy && rat.ei >= 0.2) {

    x <- x[!duplicated(xx), ]

    x <- x[rownames(x) %in% myDict[, "ENTREZID"], ]

    tmpDict <- myDict$ENSEMBL

    names(tmpDict) <- myDict$ENTREZID

    rownames(x) <- as.character(tmpDict[rownames(x)])

  } else if (rat.ei < rat.sy && rat.sy >= 0.2) {

    x <- x[!duplicated(xx), ]

    x <- x[rownames(x) %in% myDict[, "SYMBOL"], ]

    tmpDict <- myDict$ENSEMBL

    names(tmpDict) <- myDict$SYMBOL

    rownames(x) <- as.character(tmpDict[rownames(x)])

  } else {

    message("Feat ID Conversion could not be performed")

  }

  return(x)

}

#' Convert Single Cell Data Objects to DISCBIO.

#'

#' Initialize a DISCBIO-class object starting from a

#' SingleCellExperiment object or a Seurat object

#'

#' @param x an object of class Seurat or SingleCellExperiment

#' @param ... additional parameters to pass to the function

#'

#' @details Additional parameters to pass to `list` include, if x is

#'   a Seurat object, "assay", which is a string indicating the assay slot

#'   used to obtain data from (defaults to 'RNA')

#'

#' @return a DISCBIO-class object

#'

#' @export

#'

as.DISCBIO <- function(x, ...) {

  if ("Seurat" %in% class(x)) {

    # Get Arguments and parse out what we want

    all.args <- list(...)

    # Fetch arguments we care about

    if ("assay" %in% all.args) {

      assay <- all.args[["assay"]]

    } else {

      assay <- "RNA"

    }

    # Get feats and sample names

    all.feats <- base::as.character(

      rownames(x@assays[[assay]]@meta.features)

    )

    all.cells <- base::as.character(rownames(x@meta.data))

    # Get data

    all.counts <- base::data.frame(

      base::as.matrix(x@assays[[assay]]@counts)

    )

    # re-write row and colnames

    rownames(all.counts) <- all.feats

    colnames(all.counts) <- all.cells

    # prep output and return

    if (sum(grepl("^ENS", all.feats)) / length(all.feats) < 0.5) {

      all.counts <- customConvertFeats(all.counts)

    }

    y <- DISCBIO(all.counts)

  } else if ("SingleCellExperiment" %in% class(x)) {

    y <- DISCBIO(x)

  } else {

    stop("Conversion not supported")

  }

  return(y)

}

#' Convert a DISCBIO object to a SingleCellExperiment.

#'

#' Extract the SingleCellExperiment input data from the corresponding input slot

#' in a DISCBIO-class object

#'

#' @param x an object of class DISCBIO

#'

#' @return a SingleCellExperiment-class object

#'

#' @export

#' @examples

#' g1_disc <- DISCBIO(valuesG1msTest)

#' class(g1_disc)

#' g1_sce <- DISCBIO2SingleCellExperiment(g1_disc)

#' class(g1_sce)

#'

DISCBIO2SingleCellExperiment <- function(x) {

  return(x@SingleCellExperiment)

}