BSseqTstat and BSseqStat extend GRanges instead of hasGRanges

DESCRIPTION

@@ -56,7 +56,6 @@ Suggests:
     tidyverse
 Collate:
     utils.R
-    hasGRanges.R
     BSseq-class.R
     BSseqTstat_class.R
     MethylCounts.R

NAMESPACE

@@ -55,12 +55,10 @@ importFrom(R.utils, "isGzipped", "isBzipped", "gunzip", "bunzip2")
 ## Exporting
 ##
 
-exportClasses("hasGRanges",
-              "BSseq",
+exportClasses("BSseq",
               "BSseqTstat",
               "BSseqStat",
-              "MethylCounts",
-              "matrixOrNULL")
+              "MethylCounts")
 
 exportMethods("[", "show",
               "seqnames", "seqnames<-",

R/BSmooth.R

@@ -1,7 +1,7 @@
 # Internal functions -----------------------------------------------------------
 
-.rowTickmarks <- function(hasGRanges, maxGap) {
-    gr <- granges(hasGRanges)
+.rowTickmarks <- function(BSseq, maxGap) {
+    gr <- granges(BSseq)
     # NOTE: This relies on 'gr' being sorted, so really want to be sure of this!
     stopifnot(!is.unsorted(gr))
     clusters <- reduce(gr, min.gapwidth = maxGap, with.revmap = TRUE)
@@ -13,7 +13,7 @@
 makeClusters <- function(hasGRanges, maxGap = 10^8) {
     chrOrder <- as.character(runValue(seqnames(hasGRanges)))
     if(anyDuplicated(chrOrder))
-        stop("argument 'hasGRanges' is not properly order")
+        stop("argument 'hasGRanges' is not properly ordered")
     grBase <- granges(hasGRanges)
     clusters <- reduce(resize(grBase, width = 2*maxGap + 1, fix = "center"))
     start(clusters) <- pmax(rep(1, length(clusters)), start(clusters))

R/BSmooth.fstat.R

@@ -53,7 +53,7 @@ smoothSds <- function(BSseqStat, k = 101, qSd = 0.75, mc.cores = 1,
         stop("need to set argument 'maxGap'")
     if(verbose) cat("[smoothSds] preprocessing ... ")
     ptime1 <- proc.time()
-    clusterIdx <- makeClusters(granges(BSseqStat), maxGap = maxGap)
+    clusterIdx <- makeClusters(BSseqStat, maxGap = maxGap)
     ptime2 <- proc.time()
     stime <- (ptime2 - ptime1)[3]
     if(verbose) cat(sprintf("done in %.1f sec\n", stime))
@@ -137,7 +137,7 @@ localCorrectStat <- function(BSseqStat, threshold = c(-15,15), mc.cores = 1, ver
     maxGap <- BSseqStat$parameters$maxGap
     if(verbose) cat("[BSmooth.tstat] preprocessing ... ")
     ptime1 <- proc.time()
-    clusterIdx <- makeClusters(BSseqStat$gr, maxGap = maxGap)
+    clusterIdx <- makeClusters(BSseqStat, maxGap = maxGap)
     ptime2 <- proc.time()
     stime <- (ptime2 - ptime1)[3]
     if(verbose) cat(sprintf("done in %.1f sec\n", stime))

R/BSseqStat_class.R

@@ -1,4 +1,4 @@
-setClass("BSseqStat", contains = "hasGRanges",
+setClass("BSseqStat", contains = "GRanges",
          representation(stats = "list",
                         parameters = "list")
          )
@@ -9,7 +9,7 @@ setValidity("BSseqStat", function(object) {
        anyDuplicated(names(object@stats)))
         msg <- validMsg(msg, "the 'stats' list needs to be named with unique names.")
     for(name in c("rawSds", "smoothsSds", "stat", "rawTstats")) {
-        if(name %in% names(object@stats) && isTRUE(nrow(object@stats[[name]]) != length(object@gr)))
+        if(name %in% names(object@stats) && isTRUE(nrow(object@stats[[name]]) != length(object)))
             msg <- validMsg(msg, sprintf("component '%s' of slot 'stats' has to have the same number of rows as slot 'gr' is long", name))
     }
     if(is.null(msg)) TRUE else msg
@@ -24,11 +24,7 @@ setMethod("show", signature(object = "BSseqStat"),
           })
 
 setMethod("[", "BSseqStat", function(x, i, ...) {
-    if(missing(i))
-        stop("need [i] for subsetting")
-    if(missing(i))
-        return(x)
-    x@gr <- x@gr[i]
+    i <- normalizeSingleBracketSubscript(i, x)
     statnames <- names(x@stats)
     names(statnames) <- statnames
     x@stats <- lapply(statnames, function(nam) {
@@ -38,17 +34,32 @@ setMethod("[", "BSseqStat", function(x, i, ...) {
         }
         x@stats[[nam]]
     })
-    x
+    callNextMethod()
 })
 
 BSseqStat <- function(gr = NULL, stats = NULL, parameters = NULL) {
-    out <- new("BSseqStat")
-    out@gr <- gr
-    out@stats <- stats
-    out@parameters <- parameters
-    out
+    new("BSseqStat", gr, stats = stats, parameters = parameters)
 }
 
+setMethod("updateObject", "BSseqStat",
+    function(object, ..., verbose = FALSE) {
+        if (!.hasSlot(object, "gr")) {
+            return(callNextMethod())
+        }
+        if (verbose)
+            message("[updateObject] ", class(object), " object ",
+                    "uses old internal representation from\n",
+                    "[updateObject] bsseq <= 1.49.2. ",
+                    "Updating it ... ", appendLF=FALSE)
+        gr <- updateObject(object@gr)
+        ans <- BSseqStat(gr = gr, stats = object@stats,
+                                  parameters = object@parameters)
+        if (verbose)
+            message("OK")
+        ans
+    }
+)
+
 # TODO: updateObject() to use ordinary matrix instead of DelayedMatrix with
 #       in-memory seed.
 # setMethod("updateObject", "BSseqStat",

R/BSseqTstat_class.R

@@ -1,11 +1,14 @@
-setClass("BSseqTstat", contains = "hasGRanges",
-         representation(stats = "matrix",
+## Add new union members as needed (e.g. "SparseMatrix").
+setClassUnion("matrix_OR_DelayedMatrix", c("matrix", "DelayedMatrix"))
+
+setClass("BSseqTstat", contains = "GRanges",
+         representation(stats = "matrix_OR_DelayedMatrix",
                         parameters = "list")
          )
 setValidity("BSseqTstat", function(object) {
     msg <- NULL
-    if(length(object@gr) != nrow(object@stats))
-        msg <- c(msg, "length of 'gr' is different from the number of rows of 'stats'")
+    if(length(object) != nrow(object@stats))
+        msg <- c(msg, "'stats' must have one row per methylation locus")
     if(is.null(msg)) TRUE else msg
 })
 
@@ -20,21 +23,13 @@ setMethod("show", signature(object = "BSseqTstat"),
           })
 
 setMethod("[", "BSseqTstat", function(x, i, ...) {
-    if(missing(i))
-        stop("need [i] for subsetting")
-    if(missing(i))
-        return(x)
-    x@gr <- x@gr[i]
+    i <- normalizeSingleBracketSubscript(i, x)
     x@stats <- x@stats[i,, drop = FALSE]
-    x
+    callNextMethod()
 })
 
 BSseqTstat <- function(gr = NULL, stats = NULL, parameters = NULL) {
-    out <- new("BSseqTstat")
-    out@gr <- gr
-    out@stats <- stats
-    out@parameters <- parameters
-    out
+    new("BSseqTstat", gr, stats = stats, parameters = parameters)
 }
 
 summary.BSseqTstat <- function(object, ...) {
@@ -68,10 +63,20 @@ plot.BSseqTstat <- function(x, y, ...) {
 }
 
 setMethod("updateObject", "BSseqTstat",
-          function(object, ...) {
-              stats <- object@stats
-              stats <- stats
-              object@stats <- stats
-              object
-          }
+    function(object, ..., verbose = FALSE) {
+        if (!.hasSlot(object, "gr")) {
+            return(callNextMethod())
+        }
+        if (verbose)
+            message("[updateObject] ", class(object), " object ",
+                    "uses old internal representation from\n",
+                    "[updateObject] bsseq <= 1.49.2. ",
+                    "Updating it ... ", appendLF=FALSE)
+        gr <- updateObject(object@gr)
+        ans <- BSseqTstat(gr = gr, stats = object@stats,
+                                   parameters = object@parameters)
+        if (verbose)
+            message("OK")
+        ans
+    }
 )

man/BSseqStat-class.Rd

@@ -17,9 +17,11 @@
 }
 \arguments{
     \item{gr}{The genomic locations as an object of class \code{GRanges}.}
-    \item{stats}{The statistics, as a list of matrix-like objects (see
-        'Details' below).}
-    \item{parameters}{A list of parameters.}
+    \item{stats}{A list of matrix-like objects (see 'Details' below) with
+      list elements representing various statistics for methylation loci
+      along the genome.}
+    \item{parameters}{A list of parameters, as an object of class \code{list},
+      representing how the statistics were computed.}
 }
 \details{
     The matrix-like elements of the list in the 'stats' slot will be
@@ -35,19 +37,8 @@
     However, usually objects are returned by \code{BSmooth.fstat(...)} and
     not constructed by the user.
 }
-\section{Slots}{
-  \describe{
-    \item{\code{stats}:}{This is a list of   \code{\link[DelayedArray]{DelayedMatrix}}
-      objects with list elements representing various statistics for
-      methylation loci along the genome.}
-    \item{\code{parameters}:}{Object of class \code{list}.  A list of
-      parameters representing how the statistics were computed.}
-    \item{\code{gr}:}{Object of class \code{GRanges} giving genomic
-      locations.}
-  }
-}
 \section{Extends}{
-    Class \code{\linkS4class{hasGRanges}}, directly.
+    Class \code{\link[GenomicRanges]{GRanges}}, directly.
 }
 \section{Methods}{
     \describe{
@@ -57,10 +48,11 @@
     }
 }
 \section{Utilities}{
-    This class extends \code{hasGRanges} and therefore inherits a number
-    of useful \code{GRanges} methods that operate on the \code{gr} slot,
-    used for accessing and setting the genomic locations and also do
-    \code{subsetByOverlaps}.
+    This class extends \code{\link[GenomicRanges]{GRanges}} and therefore
+    inherits the full \code{GRanges} API. This means that \code{BSseqStat}
+    objects support any operation supported by \code{GRanges} objects, like
+    \code{seqnames}, \code{start}, \code{end}, \code{width}, \code{strand},
+    \code{[}, \code{findOverlaps}, \code{subsetByOverlaps}, etc...
 }
 \section{Coercion}{
   Package version 1.11.1 introduced a new version of representing
@@ -71,7 +63,8 @@
     Kasper Daniel Hansen \email{khansen@jhsph.edu}
 }
 \seealso{
-    \code{\linkS4class{hasGRanges}} for accessing the genomic locations.
+    \code{\link[GenomicRanges]{GRanges}} in the \pkg{GenomicRanges} package
+    for accessing the genomic locations.
     \code{\link{BSmooth.fstat}} for a function
     that returns objects of class \code{BSseqStat}, and \code{\link{smoothSds}},
     \code{\link{computeStat}} and \code{\link{dmrFinder}}