@@ -4,7 +4,7 @@ Description: The SummarizedExperiment container contains one or more assays,

 	each represented by a matrix-like object of numeric or other mode.

 	The rows typically represent genomic ranges of interest and the columns

 	represent samples.

-Version: 1.3.2

+Version: 1.3.3

 Encoding: UTF-8

 Author: Martin Morgan, Valerie Obenchain, Jim Hester, Hervé Pagès 

 Maintainer: Bioconductor Package Maintainer <[email protected]>

@@ -12,14 +12,13 @@ biocViews: Genetics, Infrastructure, Sequencing, Annotation, Coverage,

 	GenomeAnnotation

 Depends: R (>= 3.2), methods, GenomicRanges (>= 1.23.15), Biobase

 Imports: utils, stats, BiocGenerics (>= 0.15.3), S4Vectors (>= 0.9.36),

-	IRanges (>= 2.5.26), GenomeInfoDb

+	IRanges (>= 2.7.2), GenomeInfoDb

 Suggests: annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures,

 	TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle, knitr, rmarkdown,

 	digest, jsonlite, rhdf5, airway

 VignetteBuilder: knitr

 License: Artistic-2.0

-Collate: utils.R

-	Assays-class.R

+Collate: Assays-class.R

 	SummarizedExperiment-class.R

 	RangedSummarizedExperiment-class.R

 	intra-range-methods.R

@@ -84,7 +84,6 @@ export(

 ###

 export(

-    arbind, acbind,

     SummarizedExperiment,

     exptData, "exptData<-",

     rowRanges, "rowRanges<-",

@@ -97,7 +96,6 @@ export(

 ### Exactly the same list as above.

 exportMethods(

-    arbind, acbind,

     SummarizedExperiment,

     exptData, "exptData<-",

     rowRanges, "rowRanges<-",

@@ -227,12 +227,6 @@ setReplaceMethod("[", "Assays",

 ### rbind/cbind

-setGeneric("arbind", function(...) standardGeneric("arbind"))

-setGeneric("acbind", function(...) standardGeneric("acbind"))

-

-setMethod("arbind", "array", arbind_default)

-setMethod("acbind", "array", acbind_default)

-

 .bind_Assays <- function(lst, bind)

 {

     if (length(lst) == 0L)

deleted file mode 100644

@@ -1,128 +0,0 @@

-### =========================================================================

-### Some low-level utils

-### -------------------------------------------------------------------------

-###

-### Unless stated otherwise, nothing in this file is exported.

-###

-

-

-### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

-### Bind arrays with an arbitrary number of dimensions along the 1st or 2nd

-### dimension

-###

-

-### Return a matrix with one row per dim and one column per object.

-.get_and_check_objects_dims <- function(objects, no.check.along)

-{

-    dims <- lapply(objects, dim)

-    ndims <- lengths(dims)

-    ndim <- ndims[[1L]]

-    if (!all(ndims == ndim))

-        stop("all the objects to bind must have the same nb of dimensions")

-    tmp <- unlist(dims, use.names=FALSE)

-    if (is.null(tmp))

-        stop("the objects to bind have no dimensions")

-    dims <- matrix(tmp, nrow=ndim)

-    tmp <- dims[-no.check.along, , drop=FALSE]

-    if (!all(tmp == tmp[ , 1L]))

-        stop("objects to bind have incompatible dimensions")

-    dims

-}

-

-### 'objects' is assumed to be a list of vector-like objects.

-### 'block_lens' is assumed to be an integer vector parallel to 'objects'

-### specifying the block length for each object in 'objects'. In addition the

-### length of 'object[[i]]' must be 'k * block_lens[[i]]' (k is the same for

-### all the objects).

-.intertwine_blocks <- function(objects, block_lens)

-{

-    data <- unlist(objects, recursive=FALSE, use.names=FALSE)

-    objects_lens <- lengths(objects)

-    if (all(objects_lens == 0L))

-        return(data)

-

-    k <- objects_lens %/% block_lens

-    k <- unique(k[!is.na(k)])

-    stopifnot(length(k) == 1L)  # sanity check

-

-    nobject <- length(objects)

-    objects_cumlens <- cumsum(objects_lens)

-    ranges <- lapply(seq_len(nobject),

-        function(i) {

-            width <- block_lens[[i]]

-            offset <- if (i == 1L) 0L else objects_cumlens[[i - 1L]]

-            successiveIRanges(rep.int(width, k), from=offset + 1L)

-        })

-    ranges <- do.call(c, ranges)

-    i <- as.vector(matrix(seq_len(nobject * k), nrow=nobject, byrow=TRUE))

-    extractROWS(data, ranges[i])

-}

-

-.combine_dimnames <- function(objects, dims, along)

-{

-    ndim <- nrow(dims)

-    dimnames <- lapply(seq_len(ndim),

-        function(n) {

-            for (x in objects) {

-                dn <- dimnames(x)[[n]]

-                if (!is.null(dn))

-                    return(dn)

-            }

-            NULL

-        })

-    along_names <- lapply(objects, function(x) dimnames(x)[[along]])

-    along_names_lens <- lengths(along_names)

-    if (any(along_names_lens != 0L)) {

-        fix_idx <- which(along_names_lens != dims[along, ])

-        along_names[fix_idx] <- lapply(dims[along, fix_idx], character)

-    }

-    along_names <- unlist(along_names, use.names=FALSE)

-    if (!is.null(along_names))

-        dimnames[[along]] <- along_names

-    if (all(S4Vectors:::sapply_isNULL(dimnames)))

-        dimnames <- NULL

-    dimnames

-}

-

-### A stripped-down version of abind::abind().

-### Some differences:

-###   (a) Treatment of dimnames: .simple_abind() treatment of dimnames is

-###       consistent with base::rbind() and base::cbind(). This is not the

-###       case for abind::abind() which does some strange things with the

-###       dimnames.

-###   (b) Performance: .simple_abind() has a little bit more overhead than

-###       abind::abind(). This makes it slower on small objects. However it

-###       tends to be slightly faster on big objects.

-.simple_abind <- function(..., along)

-{

-    objects <- list(...)

-    object_is_NULL <- S4Vectors:::sapply_isNULL(objects)

-    if (any(object_is_NULL))

-        objects <- objects[!object_is_NULL]

-    if (length(objects) == 0L)

-        return(NULL)

-    if (length(objects) == 1L)

-        return(objects[[1L]])

-

-    ## Check dim compatibility.

-    dims <- .get_and_check_objects_dims(objects, no.check.along=along)

-

-    ## Perform the binding.

-    block_lens <- dims[along, ]

-    for (n in seq_len(along - 1L))

-        block_lens <- block_lens * dims[n, ]

-    ans <- .intertwine_blocks(objects, block_lens)

-

-    ## Set the dim.

-    ans_dim <- dims[ , 1L]

-    ans_dim[[along]] <- sum(dims[along, ])

-    dim(ans) <- ans_dim

-

-    ## Combine and set the dimnames.

-    dimnames(ans) <- .combine_dimnames(objects, dims, along=along)

-    ans

-}

-

-arbind_default <- function(...) .simple_abind(..., along=1L)

-acbind_default <- function(...) .simple_abind(..., along=2L)

-

deleted file mode 100644

@@ -1,96 +0,0 @@

-.TEST_matrices <- list(

-    matrix(1:15, nrow=3, ncol=5,

-           dimnames=list(NULL, paste0("M1y", 1:5))),

-    matrix(101:135, nrow=7, ncol=5,

-           dimnames=list(paste0("M2x", 1:7), paste0("M2y", 1:5))),

-    matrix(1001:1025, nrow=5, ncol=5,

-           dimnames=list(paste0("M3x", 1:5), NULL))

-)

-

-.TEST_arrays <- list(

-    array(1:60, c(3, 5, 4),

-           dimnames=list(NULL, paste0("M1y", 1:5), NULL)),

-    array(101:240, c(7, 5, 4),

-           dimnames=list(paste0("M2x", 1:7), paste0("M2y", 1:5), NULL)),

-    array(10001:10100, c(5, 5, 4),

-           dimnames=list(paste0("M3x", 1:5), NULL, paste0("M3z", 1:4)))

-)

-

-

-test_arbind_default <- function()

-{

-    arbind_default <- SummarizedExperiment:::arbind_default

-

-    ## on matrices

-    target <- do.call(rbind, .TEST_matrices)

-    current <- do.call(arbind_default, .TEST_matrices)

-    checkIdentical(target, current)

-

-    ## on empty matrices

-    m1 <- matrix(nrow=0, ncol=3, dimnames=list(NULL, letters[1:3]))

-    m2 <- matrix(1:15, ncol=3, dimnames=list(NULL, LETTERS[1:3]))

-

-    target <- do.call(rbind, list(m1, m2))

-    current <- do.call(arbind_default, list(m1, m2))

-    checkIdentical(target, current)

-

-    target <- do.call(rbind, list(m2, m1))

-    current <- do.call(arbind_default, list(m2, m1))

-    checkIdentical(target, current)

-

-    target <- do.call(rbind, list(m1, m1))

-    current <- do.call(arbind_default, list(m1, m1))

-    checkIdentical(target, current)

-

-    ## on arrays

-    current <- do.call(arbind_default, .TEST_arrays)

-    for (k in 1:4) {

-        target <- do.call(rbind, lapply(.TEST_arrays, `[`, , , k))

-        checkIdentical(target, current[ , , k])

-    }

-}

-

-test_acbind_default <- function()

-{

-    acbind_default <- SummarizedExperiment:::acbind_default

-

-    ## on matrices

-    matrices <- lapply(.TEST_matrices, t)

-    target <- do.call(cbind, matrices)

-    current <- do.call(acbind_default, matrices)

-    checkIdentical(target, current)

-

-    ## on empty matrices

-    m1 <- matrix(nrow=3, ncol=0, dimnames=list(letters[1:3], NULL))

-    m2 <- matrix(1:15, nrow=3, dimnames=list(LETTERS[1:3], NULL))

-

-    target <- do.call(cbind, list(m1, m2))

-    current <- do.call(acbind_default, list(m1, m2))

-    checkIdentical(target, current)

-

-    target <- do.call(cbind, list(m2, m1))

-    current <- do.call(acbind_default, list(m2, m1))

-    checkIdentical(target, current)

-

-    target <- do.call(cbind, list(m1, m1))

-    current <- do.call(acbind_default, list(m1, m1))

-    checkIdentical(target, current)

-

-    ## on arrays

-

-    ## transpose the 1st 2 dimensions

-    arrays <- lapply(.TEST_arrays,

-        function(a) {

-            a_dimnames <- dimnames(a)

-            dim(a)[1:2] <- dim(a)[2:1]

-            a_dimnames[1:2] <- a_dimnames[2:1]

-            dimnames(a) <- a_dimnames

-            a

-    })

-    current <- do.call(acbind_default, arrays)

-    for (k in 1:4) {

-        target <- do.call(cbind, lapply(arrays, `[`, , , k))

-        checkIdentical(target, current[ , , k])

-    }

-}

-

@@ -12,10 +12,6 @@

 \alias{dim,Assays-method}

 \alias{[,Assays,ANY-method}

 \alias{[<-,Assays,ANY,ANY,ANY-method}

-\alias{arbind}

-\alias{acbind}

-\alias{arbind,array-method}

-\alias{acbind,array-method}

 \alias{rbind,Assays-method}

 \alias{cbind,Assays-method}