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# Exported classes -------------------------------------------------------------
# NOTE: This create a 'classGeneratorFunction' (internal constructor), .BSseq()
.BSseq <- setClass(
"BSseq",
slots = representation(
trans = "function",
parameters = "list"),
contains = "RangedSummarizedExperiment"
)
# Validity methods -------------------------------------------------------------
.checkAssayNames <- function(object, names) {
if (all(names %in% assayNames(object))) {
return(NULL)
} else {
paste0(
"object of class ",
class(object),
" needs to have assay slots with names ",
paste0(names, collapse = ", "))
}
}
.checkMandCov <- function(M, Cov) {
msg <- NULL
validMsg(msg, .Call(cxx_check_M_and_Cov, M, Cov))
}
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# TODO: Benchmark validity method
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setValidity2("BSseq", function(object) {
msg <- NULL
if (identical(object, .BSseq())) {
# No validity checks for object returned by internal constructor
return(msg)
}
msg <- validMsg(msg, .checkAssayNames(object, c("Cov", "M")))
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msg <- validMsg(
msg = msg,
result = .checkMandCov(
M = assay(object, "M", withDimnames = FALSE),
Cov = assay(object, "Cov", withDimnames = FALSE)))
if (is.null(msg)) {
TRUE
} else {
msg
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}
})
# Internal functions -----------------------------------------------------------
.oldTrans <- function(x) {
y <- x
ix <- which(x < 0)
ix2 <- which(x > 0)
y[ix] <- exp(x[ix])/(1 + exp(x[ix]))
y[ix2] <- 1/(1 + exp(-x[ix2]))
y
}
# Exported functions -----------------------------------------------------------
# TODO: BSseq() is arguably a bad constructor. It doesn't return a valid BSseq
# object when called without any arguments. It also does some pretty
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# complicated parsing of the inputs. But we're stuck with it because it's
# been around for a long time.
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BSseq <- function(M = NULL, Cov = NULL, coef = NULL, se.coef = NULL,
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trans = NULL, parameters = NULL, pData = NULL, gr = NULL,
pos = NULL, chr = NULL, sampleNames = NULL,
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rmZeroCov = FALSE) {
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# Argument checks ----------------------------------------------------------
# Process assays.
# NOTE: Nothing to do for 'coef', and 'se.coef'.
if (is.null(M) || is.null(Cov)) {
stop("Need 'M' and 'Cov'.")
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}
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# Process 'trans' and 'parameters'.
if (is.null(trans)) {
trans <- function(x) NULL
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}
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if (is.null(parameters)) {
parameters <- list()
}
# Process 'sampleNames' and 'pData'.
if (is.null(sampleNames)) {
if (is.null(pData)) {
# BSseq object will have no colnames.
pData <- S4Vectors:::new_DataFrame(nrows = ncol(M))
} else {
# BSseq object will have 'sampleNames' as colnames.
pData <- DataFrame(row.names = sampleNames)
}
} else {
if (is.null(pData)) {
# BSseq object will have 'sampleNames' as colnames.
pData <- DataFrame(row.names = sampleNames)
} else {
if (is.null(rownames(pData))) {
rownames(pData) <- sampleNames
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} else {
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stopifnot(identical(rownames(pData), sampleNames))
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}
}
}
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# Process 'gr', 'pos', and 'chr'.
if (is.null(gr)) {
if (is.null(pos) || is.null(chr)) {
stop("Need 'pos' and 'chr' if 'gr' not supplied.")
}
gr <- GRanges(seqnames = chr, ranges = IRanges(start = pos, width = 1L))
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}
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if (!is(gr, "GRanges")) {
stop("'gr' needs to be a GRanges.")
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}
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# Process 'rmZeroCov'.
stopifnot(isTRUEorFALSE(rmZeroCov))
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|
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# Collapse duplicate loci --------------------------------------------------
is_duplicated <- duplicated(gr)
if (any(is_duplicated)) {
warning("Detected duplicate loci. Collapsing counts in 'M' and 'Cov' ",
"at these positions.")
if (!is.null(coef) || !is.null(se.coef)) {
stop("Cannot collapse when 'coef' or 'se.coef' are non-NULL.")
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}
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loci <- gr[!is_duplicated]
ol <- findOverlaps(gr, loci, type = "equal")
M <- rowsum(x = M, group = subjectHits(ol), reorder = FALSE)
rownames(M) <- NULL
Cov <- rowsum(x = Cov, group = subjectHits(ol), reorder = FALSE)
rownames(Cov) <- NULL
} else {
loci <- gr
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}
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# Optionally, remove positions with zero coverage --------------------------
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if (rmZeroCov) {
loci_with_zero_cov <- rowAlls(Cov, value = 0)
if (any(loci_with_zero_cov)) {
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loci_with_nonzero_cov <- !loci_with_zero_cov
gr <- gr[loci_with_nonzero_cov]
M <- M[loci_with_nonzero_cov, , drop = FALSE]
Cov <- Cov[loci_with_nonzero_cov, , drop = FALSE]
coef <- coef[loci_with_nonzero_cov, , drop = FALSE]
se.coef <- se.coef[loci_with_nonzero_cov, , drop = FALSE]
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}
}
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# Construct BSseq object ---------------------------------------------------
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assays <- SimpleList(M = M, Cov = Cov, coef = coef, se.coef = se.coef)
assays <- assays[!S4Vectors:::sapply_isNULL(assays)]
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se <- SummarizedExperiment(
assays = assays,
rowRanges = loci,
colData = pData)
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.BSseq(se, trans = trans, parameters = parameters)
}
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# Move to BSseq-utils?
hasBeenSmoothed <- function(BSseq) {
"coef" %in% assayNames(BSseq)
}
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# Move to BSseq-utils?
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getBSseq <- function(BSseq,
type = c("Cov", "M", "gr", "coef", "se.coef", "trans",
"parameters"),
withDimnames = TRUE) {
type <- match.arg(type)
if (type %in% c("M", "Cov")) {
return(assay(BSseq, type, withDimnames = withDimnames))
}
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if (type %in% c("coef", "se.coef")) {
if (type %in% assayNames(BSseq)) {
return(assay(BSseq, type, withDimnames = withDimnames))
} else {
return(NULL)
}
}
if (type == "trans") {
return(BSseq@trans)
}
if (type == "parameters") {
return(BSseq@parameters)
}
if (type == "gr") {
return(BSseq@rowRanges)
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}
}
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# Move to BSseq-utils?
strandCollapse <- function(BSseq, shift = TRUE, BPPARAM = bpparam(),
BACKEND = getRealizationBackend(),
dir = tempfile("BSseq"), replace = FALSE,
chunkdim = NULL, level = NULL,
type = c("double", "integer")) {
# Argument checks ----------------------------------------------------------
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if (all(runValue(strand(BSseq)) == "*")) {
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warning("All loci are unstranded, nothing to collapse.", call. = FALSE)
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return(BSseq)
}
if (!(all(runValue(strand(BSseq)) %in% c("+", "-")))) {
stop("'BSseq' object has a mix of stranded and unstranded loci.")
}
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# Register 'BACKEND' and return to current value on exit.
# TODO: Is this strictly necessary?
current_BACKEND <- getRealizationBackend()
on.exit(setRealizationBackend(current_BACKEND), add = TRUE)
setRealizationBackend(BACKEND)
# Check compatability of 'BPPARAM' with 'BACKEND'.
if (!.areBackendsInMemory(BACKEND)) {
if (!.isSingleMachineBackend(BPPARAM)) {
stop("The parallelisation strategy must use a single machine ",
"when using an on-disk realization backend.\n",
"See help(\"read.bismark\") for details.",
call. = FALSE)
}
} else {
if (!is.null(BACKEND)) {
# NOTE: Currently do not support any in-memory realization
# backends. If the realization backend is NULL then an
# ordinary matrix is returned rather than a matrix-backed
# DelayedMatrix.
stop("The '", BACKEND, "' realization backend is not supported.",
"\n See help(\"read.bismark\") for details.",
call. = FALSE)
}
}
# If using HDF5Array as BACKEND, check remaining options are sensible.
if (identical(BACKEND, "HDF5Array")) {
# NOTE: Most of this copied from
# HDF5Array::saveHDF5SummarizedExperiment().
if (!isSingleString(dir)) {
stop(wmsg("'dir' must be a single string specifying the path to ",
"the directory where to save the BSseq object (the ",
"directory will be created)."))
}
if (!isTRUEorFALSE(replace)) {
stop("'replace' must be TRUE or FALSE")
}
HDF5Array:::.create_dir(dir = dir, replace = replace)
h5_path <- file.path(dir, "assays.h5")
} else if (identical(BACKEND, NULL)) {
h5_path <- NULL
}
# Collapse loci ------------------------------------------------------------
loci <- rowRanges(BSseq)
if (shift) {
loci <- shift(loci, shift = as.integer(-1L * (strand(loci) == "-")))
}
collapsed_loci <- reduce(loci, min.gapwidth = 0L, ignore.strand = TRUE)
# Collapse 'M' and 'Cov' matrices ------------------------------------------
ol <- findOverlaps(loci, collapsed_loci, type = "equal")
group <- subjectHits(ol)
M <- rowsum(
x = assay(BSseq, "M", withDimnames = FALSE),
group = group,
# NOTE: reorder = TRUE to ensure same row-order as collapsed_loci.
reorder = TRUE,
BPPARAM = BPPARAM,
filepath = h5_path,
name = "Cov",
chunkdim = chunkdim,
level = level,
type = type)
Cov <- rowsum(
x = assay(BSseq, "Cov", withDimnames = FALSE),
group = group,
# NOTE: reorder = TRUE to ensure same row-order as collapsed_loci.
reorder = TRUE,
BPPARAM = BPPARAM,
filepath = h5_path,
name = "Cov",
chunkdim = chunkdim,
level = level,
type = type)
# Construct BSseq object, saving it if it is HDF5-backed -------------------
se <- SummarizedExperiment(
assays = SimpleList(M = unname(M), Cov = unname(Cov)),
rowRanges = collapsed_loci,
colData = colData(BSseq))
# TODO: Is there a way to use the internal constructor with `check = FALSE`?
# Assuming input was valid, the output is valid, too.
# .BSseq(se, trans = function(x) NULL, parameters = list())
bsseq <- new2("BSseq", se, check = FALSE)
if (!is.null(BACKEND) && BACKEND == "HDF5Array") {
# NOTE: Save BSseq object; mimicing
# HDF5Array::saveHDF5SummarizedExperiment().
x <- bsseq
x@assays <- HDF5Array:::.shorten_h5_paths(x@assays)
saveRDS(x, file = file.path(dir, "se.rds"))
}
bsseq
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}
# Exported methods -------------------------------------------------------------
setMethod("show", signature(object = "BSseq"), function(object) {
cat("An object of type 'BSseq' with\n")
cat(" ", nrow(object), "methylation loci\n")
cat(" ", ncol(object), "samples\n")
if (hasBeenSmoothed(object)) {
cat("has been smoothed with\n")
cat(" ", object@parameters$smoothText, "\n")
} else {
cat("has not been smoothed\n")
}
if (.isHDF5ArrayBacked(object)) {
cat("Some assays are HDF5Array-backed\n")
} else {
cat("All assays are in-memory\n")
}
})
setMethod("pData", "BSseq", function(object) {
object@colData
})
setReplaceMethod(
"pData",
signature = signature(object = "BSseq", value = "data.frame"),
function(object, value) {
colData(object) <- as(value, "DataFrame")
object
}
)
setReplaceMethod(
"pData",
signature = signature(object = "BSseq", value = "DataFrame"),
function(object, value) {
colData(object) <- value
object
}
)
setMethod("sampleNames", "BSseq", function(object) colnames(object))
setReplaceMethod(
"sampleNames",
signature = signature(object = "BSseq", value = "ANY"),
function(object, value) {
colnames(object) <- value
object
}
)
setMethod("updateObject", "BSseq",
function(object, ...) {
# NOTE: identical() is too strong
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if (hasBeenSmoothed(object) &
isTRUE(all.equal(getBSseq(object, "trans"), .oldTrans))) {
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object@trans <- plogis
}
if (is(object, "SummarizedExperiment")) {
# NOTE: Call method for SummarizedExperiment objects
object <- callNextMethod()
return(object)
} else {
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BSseq(
gr = object@gr,
M = object@M,
Cov = object@Cov,
coef = object@coef,
se.coef = object@se.coef,
trans = object@trans,
parameters = object@parameters,
pData = object@phenoData@data)
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}
}
)
|
