R/misc.R

In plger/scDblFinder: scDblFinder

.tablevec <- function(x){
  if(!is(x, "table")) x <- table(x)
  y <- as.numeric(x)
  names(y) <- names(x)
  y
}

.getMostLikelyOrigins <- function(knn, known.origins=NULL){
  origins <- t(vapply( seq_len(nrow(knn$orig)), FUN.VALUE=character(2),
                       FUN=function(i){
           if(all(is.na(knn$orig[i,]))) return(c(NA_character_,NA_character_))
           n <- .tablevec(knn$orig[i,])
           if(length(n)==1) return(c(names(n),FALSE))
           if(sum(n==max(n))==1) return(c(names(n)[which.max(n)],FALSE))
           x <- split(knn$distance[i,], knn$orig[i,])
           x <- sort(vapply(x,min,numeric(1)))
           if( (x[2]-x[1])/x[1] > 0.2 ) return(c(names(x)[1], FALSE))
           return(c(names(x)[1], TRUE))
                       }))
  origins <- as.data.frame(origins)
  colnames(origins) <- c("mostLikelyOrigin", "originAmbiguous")
  if(!is.null(known.origins)){
    w <- which(!is.na(known.origins))
    origins[w,1] <- as.character(known.origins[w])
    origins[w,2] <- "FALSE"
  }
  origins[,1] <- factor(origins[,1])
  origins[,2] <- as.logical(origins[,2])
  origins
}

#' getExpectedDoublets
#'
#' @param x A vector of cluster labels for each cell
#' @param dbr The expected doublet rate.
#' @param only.heterotypic Logical; whether to return expectations only for
#' heterotypic doublets
#'
#' @return The expected number of doublets of each combination of clusters
#'
#' @examples
#' # random cluster labels
#' cl <- sample(head(LETTERS,4), size=2000, prob=c(.4,.2,.2,.2), replace=TRUE)
#' getExpectedDoublets(cl)
#' @export
getExpectedDoublets <- function(x, dbr=NULL, only.heterotypic=TRUE){
  if(is(x,"SingleCellExperiment")){
    clusters <- x$scDblFinder.clusters
  }else{
    clusters <- x
  }
  clusters <- droplevels(as.factor(clusters))
  lvls <- levels(clusters)
  if(all(grepl("^[0-9]*$",lvls))) lvls <- as.integer(lvls)
  clusters <- as.integer(clusters)
  ncells <- length(clusters)
  if(is.null(dbr)) dbr <- (0.01*ncells/1000)
  if(length(unique(clusters))==1) return(ncells*dbr)

  cs <- table(clusters)/ncells
  expected <- (cs %*% t(cs)) * dbr * ncells
  expected <- data.frame( type1=rep(seq_along(lvls),ncol(expected)),
                          type2=rep(seq_along(lvls),each=nrow(expected)),
                          expected=as.numeric(expected) )
  if(only.heterotypic){
    expected <- expected[expected[,1]<expected[,2],]
    expected$expected <- 2*expected$expected
  }else{
    expected[,1:2] <- t(apply(expected[,1:2], 1, FUN=sort))
    expected <- aggregate(expected[,3,drop=FALSE], by=expected[,1:2], FUN=sum)
  }
  ids <- matrix(lvls[as.integer(as.matrix(expected[,1:2]))],ncol=2)
  setNames(expected$expected, paste(ids[,1], ids[,2], sep="+"))
}

.castorigins <- function(e, val=NULL){
  if(is.table(e) || is.null(dim(e))){
    e <- cbind(do.call(rbind, strsplit(names(e),"+",fixed=TRUE)),
               data.frame(val=as.numeric(e)))
  }
  if(is.null(val)) val <- rev(colnames(e))[1]
  names(n) <- n <- unique(as.character(as.matrix(e[,1:2])))
  vapply(n, FUN.VALUE=numeric(length(n)), FUN=function(x){
    vapply(n, FUN.VALUE=numeric(1), FUN=function(y){
      if(x==y) return(NA)
      w <- which(e[,1] %in% c(x,y) & e[,2] %in% c(x,y))
      if(length(w)==0) return(0)
      sum(e[w,val])
    })
  })
}

#' selFeatures
#'
#' Selects features based on cluster-wise expression or marker detection, or a
#' combination.
#'
#' @param sce A \code{\link[SummarizedExperiment]{SummarizedExperiment-class}},
#' \code{\link[SingleCellExperiment]{SingleCellExperiment-class}} with a
#' 'counts' assay.
#' @param clusters Optional cluster assignments. Should either be a vector of
#' labels for each cell.
#' @param nfeatures The number of features to select.
#' @param propMarkers The proportion of features to select from markers (rather
#' than on the basis of high expression). Ignored if `clusters` isn't given.
#' @param FDR.max The maximum marker binom FDR to be included in the selection.
#' (see \code{\link[scran]{findMarkers}}).
#'
#' @return A vector of feature (i.e. row) names.
#' @export
#'
#' @importFrom scuttle sumCountsAcrossCells
#' @importFrom scran findMarkers
#' @examples
#' sce <- mockDoubletSCE()
#' selFeatures(sce, clusters=sce$cluster, nfeatures=5)
selFeatures <- function(sce, clusters=NULL, nfeatures=1000, propMarkers=0, FDR.max=0.05){
  if(nrow(sce)<=nfeatures) return(row.names(sce))
  if(is.null(clusters)) propMarkers <- 0
  g <- c()
  if((ng <- ceiling((1-propMarkers)*nfeatures))>0){
    if(is.null(clusters)){
      g <- row.names(sce)[order(Matrix::rowMeans(counts(sce),na.rm=TRUE),
                                decreasing=TRUE)[seq_len(ng)]]
    }else{
      g <- tryCatch({
        cl.means <- as.matrix(assay(scuttle::sumCountsAcrossCells(counts(sce), clusters)))
        g <- unique(as.numeric(t(apply(cl.means, 2, FUN=function(x){
          order(x, decreasing=TRUE)[seq_len(nfeatures)]
        }))))[seq_len(ng)]
        row.names(sce)[g]
      }, error=function(e){
        g <- row.names(sce)[order(Matrix::rowMeans(counts(sce),na.rm=TRUE),
                                  decreasing=TRUE)[seq_len(ng)]]
      })
    }
  }
  if(ng==nfeatures) return(g)
  mm <- scran::findMarkers(sce, groups=clusters, test.type="binom", assay.type="counts")
	mm <- dplyr::bind_rows(lapply(mm, FUN=function(x){
	  x <- x[x$FDR<FDR.max,]
	  data.frame(gene=row.names(x), Top=x$Top, FDR=x$FDR, stringsAsFactors=FALSE)
	}), .id = "cluster")
	g2 <- unique(c(g,mm$gene))
	if(length(g2)<nfeatures) return(g2)
	i <- nfeatures/(2*length(unique(clusters)))
	while(length(g <- unique(c(g,mm$gene[mm$Top<=i])))<nfeatures) i<-i+1
	return(head(g,nfeatures))
}


#' mockDoubletSCE
#'
#' Creates a mock random single-cell experiment object with doublets
#'
#' @param ncells A positive integer vector indicating the number of cells per
#' cluster (min 2 clusters)
#' @param ngenes The number of genes to simulate. Ignored if `mus` is given.
#' @param mus A list of cluster averages.
#' @param dbl.rate The doublet rate
#' @param only.heterotypic Whether to create only heterotypic doublets
#'
#' @return A SingleCellExperiment object, with the colData columns `type`
#' indicating whether the cell is a singlet or doublet, and `cluster`
#' indicating from which cluster (or cluster combination) it was simulated.
#'
#' @export
#' @import SingleCellExperiment
#' @importFrom stats rnorm rpois
#' @examples
#' sce <- mockDoubletSCE()
mockDoubletSCE <- function(ncells=c(200,300), ngenes=200, mus=NULL,
                           dbl.rate=0.1, only.heterotypic=TRUE){
  if(length(ncells)<2)
    stop("ncells should be a positive integer vector of length >=2")
  if(is.null(names(ncells))) names(ncells)<-paste0("cluster",seq_along(ncells))
  if(is.null(mus)){
    mus <- lapply(ncells, FUN=function(x) 2^rnorm(ngenes))
  }else{
    if(!is.list(mus) || length(mus)!=length(ncells) ||
       length(unique(lengths(mus)))!=1)
      stop("If provided, `mus` should be a list of length equal to that of ",
           "`ncells`, with each slot containing a numeric vector of averages ",
           "for each gene.")
    names(mus) <- names(ncells)
  }

  # non-doublets
  counts <- do.call(cbind, lapply(seq_along(mus), FUN=function(i){
    matrix(rpois(ncells[[i]]*ngenes, mus[[i]]), nrow=ngenes)
  }))
  sce <- SingleCellExperiment(list(counts=counts),
                              colData=data.frame(type="singlet",
                                           origin=rep(names(ncells), ncells)))

  # doublets
  expected <- getExpectedDoublets(sce$origin, dbl.rate,
                                  only.heterotypic=only.heterotypic)
  simdbl <- rpois(length(expected), expected)
  if(sum(simdbl)>0){
    mus <- lapply(strsplit(names(expected),"+",fixed=TRUE), FUN=function(x){
      mus[[x[[1]]]]+mus[[x[[2]]]]
    })
    doublets <- do.call(cbind, lapply(seq_along(mus), FUN=function(i){
      matrix(rpois(simdbl[[i]]*ngenes, mus[[i]]), nrow=ngenes)
    }))
    sce2 <- SingleCellExperiment( list(counts=doublets),
                                  colData=data.frame(type="doublet",
                                          origin=rep(names(expected), simdbl)))
    sce <- cbind(sce, sce2)
  }

  # set original cluster for homotypic doublets
  sce$cluster <- factor(sce$origin, c(names(ncells),names(expected)))
  names(n) <- n <- levels(sce$cluster)
  n[paste(names(ncells),names(ncells),sep="+")] <- names(ncells)
  levels(sce$cluster) <- gsub("\\+.*","",as.character(n))
  sce$cluster <- droplevels(sce$cluster)

  colnames(sce) <- paste0("cell",seq_len(ncol(sce)))
  row.names(sce) <- paste0("gene",seq_len(ngenes))
  sce$type <- factor(sce$type, c("singlet","doublet"))
  sce
}


.checkColArg <- function(sce, x, acceptNull=TRUE){
  arg <- deparse(substitute(x))
  if(is.null(x)){
    if(!acceptNull) stop("Missing argument `",arg,"`!")
    return(NULL)
  }
  if(is.character(x) && length(x)==1){
    if(!(x %in% colnames(colData(sce))))
      stop("Could not find `", arg, "` column in colData!")
    x <- colData(sce)[[x]]
  }else if(length(x)!=ncol(sce)){
    stop("`",arg,"` should have a length equal to the number of columns in ",
         "`sce`.")
  }
  x
}
.checkPropArg <- function(x, acceptNull=TRUE){
  arg <- deparse(substitute(x))
  if( is.null(x) && acceptNull ) return(NULL)
  if(is.null(x) || length(x)!=1 || !is.numeric(x) || x>1 || x<0)
    stop("`",arg,"` should be a positive value between 0 and 1.")
  x
}

.checkProcArg <- function(processing){
  if(is.factor(processing)) processing <- as.character(processing)
  if(is.character(processing)){
    stopifnot(length(processing)==1)
    processing <- match.arg(processing, c("default","rawPCA","rawFeatures",
                                          "normFeatures", "atac"))
  }else if(!is.function(processing)){
    stop("`processing` should either be a function")
  }else if(!all(c("e", "dims") %in% names(formals(processing)))){
    stop("If a function, `processing` should have at least the arguments `e` ",
         "(count matrix) and `dims` (number of PCA dimensions required)")
  }
  processing
}

#' cxds2
#'
#' Calculates a coexpression-based doublet score using the method developed by
#' \href{https://doi.org/10.1093/bioinformatics/btz698}{Bais and Kostka 2020}.
#' This is the original implementation from the
#' \href{https://www.bioconductor.org/packages/release/bioc/html/scds.html}{scds}
#' package, but enabling scores to be calculated for all cells while the gene
#' coexpression is based only on a subset (i.e. excluding known/artificial 
#' doublets) and making it robust to low sparsity.
#'
#' @param x A matrix of counts, or a `SingleCellExperiment` containing a
#' 'counts'
#' @param whichDbls The columns of `x` which are known doublets.
#' @param ntop The number of top features to keep.
#' @param binThresh The count threshold to be considered expressed.
#' @references \url{https://doi.org/10.1093/bioinformatics/btz698}
#' @return A cxds score or, if `x` is a `SingleCellExperiment`, `x` with an
#'   added `cxds_score` colData column.
#' @export
#' @importFrom stats pbinom quantile median
#' @examples
#' sce <- mockDoubletSCE()
#' sce <- cxds2(sce)
#' # which is equivalent to
#' # sce$cxds_score <- cxds2(counts(sce))
cxds2 <- function(x, whichDbls=c(), ntop=500, binThresh=NULL){
  if(is(x,"SingleCellExperiment")){
    x$cxds_score <- cxds2(counts(x), whichDbls=whichDbls, ntop=ntop,
                          binThresh=binThresh)
    return(x)
  }
  x[is.na(x)] <- 0L
  if(is.null(binThresh)){
    # to handle datasets with very low sparsity, filter out rows with too few
    # zeros and adjust the binarization threshold
    if(is(x,"sparseMatrix")){
      pNonZero <- length(x@x)/length(x)
    }else{
      pNonZero <- sum(x>0)/length(x)
    }
    if(pNonZero>0.5){
      pNonZero <- rowSums(x>0)/ncol(x)
      x <- x[head(order(pNonZero), ntop),]
      if(is(x,"sparseMatrix")){
        binThresh <- max(1L, as.numeric(quantile(x@x, mean(pNonZero)*0.5)))
      }else{
        binThresh <- max(1L, median(x))
      }
    }else{
      binThresh <- 1L
    }
  }
  Bp <- x <- x >= binThresh
  ps <- rowMeans(x)
  if(nrow(x)>ntop){
    hvg <- order(ps * (1 - ps), decreasing=TRUE)[seq_len(ntop)]
    Bp <- x <- x[hvg, ]
    ps <- ps[hvg]
  }
  if(length(whichDbls)>0) Bp <- Bp[,-whichDbls]
  prb <- outer(ps, 1 - ps)
  prb <- prb + t(prb)
  obs <- Bp %*% (1 - Matrix::t(Bp))
  obs <- obs + Matrix::t(obs)
  S <- suppressWarnings({
    stats::pbinom(as.matrix(obs) - 1, prob = prb, size=ncol(Bp),
        lower.tail=FALSE, log.p=TRUE)
  })
  if(any(w <- is.infinite(S))){
    smin <- min(S[!is.infinite(S)])
    S[S<smin] <- smin
  }
  s <- -Matrix::colSums(x * (S %*% x))
  s <- s - min(s)
  s/max(s)
}

#' @importFrom stats cor
.clustSpearman <- function(e, clusters, nMarkers=30){
  if(is.null(dim(clusters))){
    e2 <- e[,seq_along(clusters)]
    g <- seq_len(nrow(e2))
    if(nMarkers>0 & nMarkers<nrow(e)){
      suppressWarnings(mm <- scran::findMarkers(e2, groups=clusters, test.type="binom"))
      g <- unique(unlist(lapply(mm, FUN=function(x) row.names(x)[seq_len(nMarkers)])))
    }
    e2 <- scuttle::sumCountsAcrossCells(e2[g,], ids=clusters)
    clusters <- as.matrix(assay(e2))
  }else{
    if(ncol(clusters)>500)
      warning("You're using a very large `clustCor` matrix, are you sure that the",
              "columns are cell types, and not individual cells?")
    g <- intersect(row.names(e), row.names(clusters))
    if(length(g)<5){
      warning("Too few marker genes in common between `clustCor` and the data.",
        "No correlation will be used. Consider checking that the gene identifiers match.")
      return(NULL)
    }
    clusters <- clusters[g,]
  }
  cor(as.matrix(e[g,]), clusters, method="spearman")
}

# gets a global doublet rate from samples' doublet rates
.gdbr <- function(d, dbr=NULL){
  if(!is.null(dbr)){
    if(length(dbr)==1) return(dbr)
    stopifnot(!is.null(d$sample))
    sl <- as.numeric(table(d$sample, d$src=="real")[,2])
    return(sum(dbr*sl)/sum(sl))
  }
  if(is.null(d$sample)){
    sl <- sum(d$src=="real")
  }else{
    ## estimate a global doublet rate
    sl <- as.numeric(table(d$sample, d$src=="real")[,2])
  }
  dbr <- (0.01*sl/1000)
  sum(dbr*sl)/sum(sl)
}

#' propHomotypic
#'
#' Computes the proportion of pairs expected to be made of elements from the 
#' same cluster.
#'
#' @param clusters A vector of cluster labels
#'
#' @return A numeric value between 0 and 1.
#' @export
#'
#' @examples
#' clusters <- sample(LETTERS[1:5], 100, replace=TRUE)
#' propHomotypic(clusters)
propHomotypic <- function(clusters){
  p <- as.numeric(table(clusters)/length(clusters))
  p <- p %*% t(p)
  sum(diag(p))/sum(p)
}


.defaultProcessing <- function(e, dims=NULL, doNorm=NULL){
  # skip normalization if data is too large
  if(is.null(doNorm)) doNorm <- ncol(e)<=50000
  if(doNorm){
    tryCatch({
      e <- normalizeCounts(e)
    }, error=function(er){
      warning("Error in calculating norm factors:", er)
    })
  }
  if(is.null(dims)) dims <- 20
  pca <- scater::calculatePCA(e, ncomponents=dims, subset_row=seq_len(nrow(e)),
                              ntop=nrow(e), BSPARAM=BiocSingular::IrlbaParam())
  if(is.list(pca)) pca <- pca$x
  row.names(pca) <- colnames(e)
  pca
}

.atacProcessing <- function(e, dims=NULL){
  runPCA(TFIDF(e), BSPARAM=IrlbaParam(), center=FALSE,
              rank=max(dims))$x[,seq_len(max(dims))]
}

.checkSCE <- function(sce){
  msg <- paste(
    "`sce` should be a SingleCellExperiment, a SummarizedExperiment, ",
    "or an array (i.e. matrix, sparse matric, etc.) of counts.")
  if(is(sce, "SummarizedExperiment")){
    sce <- as(sce, "SingleCellExperiment")
  }else if(!is(sce, "SingleCellExperiment")){
    if(is.null(dim(sce)) || any(sce<0)) stop(msg)
    message("Assuming the input to be a matrix of counts or expected counts.")
    sce <- SingleCellExperiment(list(counts=sce))
  }
  if( !("counts" %in% assayNames(sce)) )
    stop("`sce` should have an assay named 'counts'")
  counts(sce) <- as(counts(sce),"CsparseMatrix")
  if(any(counts(sce)<0))
    stop(msg, "\n", "The data contains negative counts!")
  if(min(colSums(counts(sce)))<200)
    warning("Some cells in `sce` have an extremely low read counts; note ",
            "that these could trigger errors and might best be filtered out")
  if(is.null(colnames(sce)))
    colnames(sce) <- paste0("cell",seq_len(ncol(sce)))
  if(any(duplicated(colnames(sce)))){
    warning("Duplicated cell names found, names were appended a suffix.")
    colnames(sce) <- make.unique(colnames(sce))
  }
  if(is.null(row.names(sce)))
    row.names(sce) <- paste0("f",seq_len(nrow(sce)))
  sce
}



# procedure to 0-1 rescale scores across samples so that the mins, maxs, and 
# trimmed mean of real and artificial cells is the same across samples; then 
# doing quantile normalization between these fixed points
.rescaleSampleScores <- function(d, byType=is.null(q), q=NULL, what="score",
                                 newName=NULL, mode=c("quantile","linear")){
  mode <- match.arg(mode)
  if(what=="score" && is.null(newName)) d$perSampleScore <- d$score
  if(is.null(newName)){
    newName <- what
  }else{
    d[[newName]] <- NA_real_
  }
  if(is.null(q)){
    if(byType){
      wD <- which(d$type=="doublet")
      q <- t(vapply(split(d[[what]], d$sample), FUN.VALUE=numeric(2L), FUN=function(x){
        sort(c(mean(x[-wD], na.rm=TRUE, trim=0.5), mean(x[wD], na.rm=TRUE, trim=0.5))) }))
      colnames(q) <- c("singlet","doublet")
    }else{
      q <- as.matrix(vapply(split(d[[what]], d$sample), FUN.VALUE=numeric(1L),
                            FUN=mean, trim=0.5, na.rm=TRUE))
    }
  }else{
    if(byType) stop("Cannot scale by type with given quantiles.")
    if(is.null(dim(q))) q <- as.matrix(q)
  }
  if(mode=="quantile"){
    .qscale <- function(x, by){
      si <- split(seq_along(x),as.character(by))
      sf <- lapply(si, ecdf)
      for(s in names(si)) x[si[[s]]] <- sf[[s]](x[si[[s]]])
      x
    }
  }else{
    .qscale <- function(x, by){
      mins <- vapply(split(x,by),FUN.VALUE=numeric(1),FUN=function(x){
        if(length(x)==0) return(0); min(x,na.rm=TRUE) })
      maxs <- vapply(split(x,by),FUN.VALUE=numeric(1),FUN=function(x){
        if(length(x)==0) return(1); max(x,na.rm=TRUE) })
      (x-mins[by])/(maxs[by]-mins[by])
    }
  }
  or.sc <- d[[what]]
  if(ncol(q)>1){
    qmeds <- apply(q,2,median)
    w <- which(or.sc <= q[d$sample,1])
    d[[newName]][w] <- .qscale(or.sc[w],by=d$sample[w])*qmeds[1]
    w <- which(or.sc > q[d$sample,1] & or.sc <=q[d$sample,2])
    d[[newName]][w] <- qmeds[1]+.qscale(or.sc[w],by=d$sample[w])*(qmeds[2]-qmeds[1])
    w <- which(or.sc > q[d$sample,2])
    d[[newName]][w] <- qmeds[2]+.qscale(or.sc[w],by=d$sample[w])*(1-qmeds[2])
    maxs <- vapply(split(d[[newName]],d$sample),FUN.VALUE=numeric(1),na.rm=TRUE,FUN=max)
    d[[newName]] <- d[[newName]]/maxs[d$sample]
  }else{
    thm <- median(q)
    ll <- split(or.sc, d$sample)
    ths <- q[d$sample,]
    w <- which(or.sc<=ths)
    d[[newName]][w] <- thm*d[[what]][w]/ths[w]
    w <- which(or.sc>ths)
    d[[newName]][w] <- thm + (d[[what]][w]-ths[w])*(1-thm)/(1-ths[w])
  }
  return(d)
}


#' directClassification
#'
#' Trains a classifier directly on the expression matrix to distinguish
#' artificial doublets from real cells.
#'
#' @param sce A \code{\link[SummarizedExperiment]{SummarizedExperiment-class}},
#' \code{\link[SingleCellExperiment]{SingleCellExperiment-class}}, or array of
#' counts.
#' @param dbr The expected doublet rate. By default this is assumed to be 1\%
#' per thousand cells captured (so 4\% among 4000 thousand cells), which is
#' appropriate for 10x datasets. Corrections for homeotypic doublets will be
#' performed on the given rate.
#' @param processing Counts (real and artificial) processing. Either
#' 'default' (normal \code{scater}-based normalization and PCA), "rawPCA" (PCA
#' without normalization), "rawFeatures" (no normalization/dimensional
#' reduction), "normFeatures" (uses normalized features, without PCA) or a
#' custom function with (at least) arguments `e` (the matrix of counts) and
#' `dims` (the desired number of dimensions), returning a named matrix with
#' cells as rows and components as columns.
#' @param dims The number of dimensions used.
#' @param nrounds Maximum rounds of boosting. If NULL, will be determined
#' through cross-validation.
#' @param max_depth Maximum depths of each tree.
#' @param iter A positive integer indicating the number of scoring iterations.
#' At each iteration, real cells that would be called as doublets are excluding
#' from the training, and new scores are calculated.
#' @param ... Any doublet generation or pre-processing argument passed to
#' `scDblFinder`.
#'
#' @return A \code{\link[SummarizedExperiment]{SummarizedExperiment-class}}
#' with the additional `colData` column `directDoubletScore`.
#' @export
#'
#' @examples
#' sce <- directDblClassification(mockDoubletSCE(), artificialDoublets=1)
#' boxplot(sce$directDoubletScore~sce$type)
directDblClassification <- function(sce, dbr=NULL, processing="default", iter=2,
                                    dims=20, nrounds=0.25, max_depth=6, ...){
  sce <- .checkSCE(sce)
  sce.full <- scDblFinder(sce, returnType="counts", dims=dims, dbr=dbr,
                          processing=processing, ...)
  e <- counts(sce.full)
  if(is.character(processing)){
    preds <- switch(processing,
                    default=.defaultProcessing(e, dims=dims),
                    rawPCA=.defaultProcessing(e, dims=dims, doNorm=FALSE),
                    rawFeatures=t(e),
                    normFeatures=t(normalizeCounts(e)),
                    stop("Unknown processing function.")
    )
  }else{
    preds <- processing(e, dims=dims)
    stopifnot(identical(row.names(preds),colnames(e)))
  }
  d <- data.frame( row.names=colnames(sce.full),
                   type=sce.full$type,
                   src=sce.full$type,
                   score=sce.full$cxds_score/max(sce.full$cxds_score, na.rm=TRUE),
                   cluster=sce.full$cluster )
  d$include.in.training <- TRUE
  rm(sce.full)
  for(i in seq_len(iter)){
    dT <- suppressWarnings(doubletThresholding(d, dbr=dbr, returnType="call"))
    w <- which( d$type=="real" & dT=="doublet" )
    message("Round ",i,": ",length(w)," excluded from training.")
    d$score <- tryCatch({
      fit <- .xgbtrain(preds[-w,], d$type[-w], nrounds, max_depth=max_depth)
      predict(fit, as.matrix(preds))
    }, error=function(e) d$score)
  }
  sce$directDoubletScore <- d[colnames(sce), "score"]
  sce
}

#' @importFrom GenomicRanges makeGRangesFromDataFrame
#' @importFrom utils read.delim
.import.bed <- function(x){
  y <- read.delim(x, header=FALSE, nrows=5, stringsAsFactors=FALSE)
  stopifnot(ncol(y)>=3)
  if(!is.character(y[,1]) || !is.integer(y[,2]) || !is.integer(y[,3]))
    stop("Malformed bed!")
  colClasses <- head(c("factor","integer","integer","factor","integer",
                       rep("NULL", ncol(y))), 
                     ncol(y))

  if(ncol(y)>4 & !is.integer(y[,5])) colClasses <- colClasses[1:4]
  x <- read.delim(x, header=FALSE, colClasses=colClasses, stringsAsFactors=TRUE)
  nc <- seq_len(min(5,ncol(x)))
  colnames(x)[nc] <- c("seqname", "start", "end", "name", "score")[nc]
  return(makeGRangesFromDataFrame(x, keep.extra.columns=TRUE))
}