R/combine-method.R

In shokoohi/DMCHMM: Differentially Methylated CpG using Hidden Markov Model

.combine.BSData <- function(obj1, obj2) {
    if (any(is.element(colnames(obj1), colnames(obj2)))) {
        stop("The BSData objects to combine should not have samples in common!")
    }
    colData.new <- rbind(colData(obj1), colData(obj2))
    rowRanges.new <- sort(unique(c(rowRanges(obj1), rowRanges(obj2))))
    ind.match.obj1 <- findOverlaps(rowRanges.new, rowRanges(obj1),
        select = "first")
    ind.match.obj2 <- findOverlaps(rowRanges.new, rowRanges(obj2),
        select = "first")
    nr <- length(rowRanges.new)
    nc <- nrow(colData.new)
    methReads.new <- matrix(integer(length = nr * nc), ncol = nc, nrow = nr,
        dimnames = list(names(rowRanges.new), rownames(colData.new)))
    methReads.new[, ] <- cbind(methReads(obj1)[ind.match.obj1, ],
        methReads(obj2)[ind.match.obj2, ])
    methReads.new[is.na(methReads.new)] <- 0L
    totalReads.new <- matrix(integer(length = nr * nc), ncol = nc, nrow = nr,
        dimnames = list(names(rowRanges.new), rownames(colData.new)))
    totalReads.new[, ] <- cbind(totalReads(obj1)[ind.match.obj1, ],
        totalReads(obj2)[ind.match.obj2, ])
    totalReads.new[is.na(totalReads.new)] <- 0L
    z <- cBSData(colData = colData.new, rowRanges = rowRanges.new,
            methReads = methReads.new, totalReads = totalReads.new)
    return(z)
}

.combine.BSDMCs <- function(obj1, obj2) {
    if (any(is.element(colnames(obj1), colnames(obj2)))) {
        stop("The BSDMCs objects to combine should not have samples in common!")
    }
    colData.new <- rbind(colData(obj1), colData(obj2))
    rowRanges.new <- sort(unique(c(rowRanges(obj1), rowRanges(obj2))))
    ind.match.obj1 <- findOverlaps(rowRanges.new, rowRanges(obj1),
        select = "first")
    ind.match.obj2 <- findOverlaps(rowRanges.new, rowRanges(obj2),
        select = "first")
    nr <- length(rowRanges.new)
    nc <- nrow(colData.new)
    methReads.new <- matrix(integer(length = nr * nc), ncol = nc, nrow = nr,
        dimnames = list(names(rowRanges.new), rownames(colData.new)))
    methReads.new[, ] <- cbind(methReads(obj1)[ind.match.obj1, ],
        methReads(obj2)[ind.match.obj2, ])
    methReads.new[is.na(methReads.new)] <- 0L
    totalReads.new <- matrix(integer(length = nr * nc), ncol = nc, nrow = nr,
        dimnames = list(names(rowRanges.new), rownames(colData.new)))
    totalReads.new[, ] <- cbind(totalReads(obj1)[ind.match.obj1, ],
                                totalReads(obj2)[ind.match.obj2, ])
    totalReads.new[is.na(totalReads.new)] <- 0L
    methStates.new <- matrix(integer(length = nr * nc), ncol = nc, nrow = nr,
        dimnames = list(names(rowRanges.new), rownames(colData.new)))
    methStates.new[, ] <- cbind(methStates(obj1)[ind.match.obj1, ],
                                methStates(obj2)[ind.match.obj2, ])
    methStates.new[is.na(methStates.new)] <- 0L
    methLevels.new <- matrix(integer(length = nr * nc), ncol = nc, nrow = nr,
        dimnames = list(names(rowRanges.new), rownames(colData.new)))
    methLevels.new[, ] <- cbind(methLevels(obj1)[ind.match.obj1, ],
                                methLevels(obj2)[ind.match.obj2, ])
    methLevels.new[is.na(methLevels.new)] <- 0L

    methVars.new <- matrix(integer(length = nr * nc), ncol = nc, nrow = nr,
        dimnames = list(names(rowRanges.new), rownames(colData.new)))
    methVars.new[, ] <- cbind(methVars(obj1)[ind.match.obj1, ],
                                methVars(obj2)[ind.match.obj2, ])
    methVars.new[is.na(methVars.new)] <- 0L

    z <- cBSDMCs(methReads = methReads.new, totalReads = totalReads.new,
        methLevels = methLevels.new, methStates = methStates.new,
        methVars = methVars.new, rowRanges = rowRanges.new,
        colData = colData.new)
    return(z)
}

#' @rdname combine-method
#' @aliases combine-method combine
setMethod("combine", signature(obj1 = "BSData", obj2="BSData"), .combine.BSData)

#' @rdname combine-method
#' @aliases combine-method combine
setMethod("combine", signature(obj1 = "BSDMCs", obj2="BSDMCs"), .combine.BSDMCs)