Virtually reshaped HDF5 datasets as DelayedArray objects
ReshapedHDF5Array-class.RdThe ReshapedHDF5Array class is a DelayedArray subclass for representing an HDF5 dataset with a user-supplied upfront virtual reshaping.
All the operations available for DelayedArray objects work on ReshapedHDF5Array objects.
Arguments
- filepath, name, type
See
?HDF5Arrayfor a description of these arguments.- dim
A vector of dimensions that describes the virtual reshaping i.e. the reshaping that is virtually applied upfront to the HDF5 dataset when the ReshapedHDF5Array object gets constructed.
Note that the HDF5 dataset is treated as read-only so is not effectively reshaped, that is, the dataset dimensions encoded in the HDF5 file are not mmodified.
Also please note that arbitrary reshapings are not supported. Only reshapings that reduce the number of dimensions by collapsing a group of consecutive dimensions into a single dimension are supported. For example, reshaping a 10 x 3 x 5 x 1000 array as a 10 x 15 x 1000 array or as a 150 x 1000 matrix is supported.
Value
A ReshapedHDF5Array (or ReshapedHDF5Matrix) object. (Note that ReshapedHDF5Matrix extends ReshapedHDF5Array.)
See also
HDF5Array objects for representing HDF5 datasets as DelayedArray objects without upfront virtual reshaping.
DelayedArray objects in the DelayedArray package.
writeHDF5Arrayfor writing an array-like object to an HDF5 file.saveHDF5SummarizedExperimentandloadHDF5SummarizedExperimentin this package (the HDF5Array package) for saving/loading an HDF5-based SummarizedExperiment object to/from disk.The ReshapedHDF5ArraySeed helper class.
h5lsto list the content of an HDF5 file.
Examples
library(h5vcData)
tally_file <- system.file("extdata", "example.tally.hfs5",
package="h5vcData")
h5ls(tally_file)
#> group name otype dclass dim
#> 0 / ExampleStudy H5I_GROUP
#> 1 /ExampleStudy 16 H5I_GROUP
#> 2 /ExampleStudy/16 Counts H5I_DATASET INTEGER 12 x 6 x 2 x 90354753
#> 3 /ExampleStudy/16 Coverages H5I_DATASET INTEGER 6 x 2 x 90354753
#> 4 /ExampleStudy/16 Deletions H5I_DATASET INTEGER 6 x 2 x 90354753
#> 5 /ExampleStudy/16 Reference H5I_DATASET INTEGER 90354753
#> 6 /ExampleStudy 22 H5I_GROUP
#> 7 /ExampleStudy/22 Counts H5I_DATASET INTEGER 12 x 6 x 2 x 51304566
#> 8 /ExampleStudy/22 Coverages H5I_DATASET INTEGER 6 x 2 x 51304566
#> 9 /ExampleStudy/22 Deletions H5I_DATASET INTEGER 6 x 2 x 51304566
#> 10 /ExampleStudy/22 Reference H5I_DATASET INTEGER 51304566
## Pick up "Coverages" dataset for Human chromosome 16 and collapse its
## first 2 dimensions:
cvg <- ReshapedHDF5Array(tally_file, "/ExampleStudy/16/Coverages",
dim=c(12, 90354753))
cvg
#> <12 x 90354753> ReshapedHDF5Matrix object of type "integer":
#> [,1] [,2] [,3] [,4] ... [,90354750]
#> [1,] 0 0 0 0 . 0
#> [2,] 0 0 0 0 . 0
#> [3,] 0 0 0 0 . 0
#> [4,] 0 0 0 0 . 0
#> [5,] 0 0 0 0 . 0
#> ... . . . . . .
#> [8,] 0 0 0 0 . 0
#> [9,] 0 0 0 0 . 0
#> [10,] 0 0 0 0 . 0
#> [11,] 0 0 0 0 . 0
#> [12,] 0 0 0 0 . 0
#> [,90354751] [,90354752] [,90354753]
#> [1,] 0 0 0
#> [2,] 0 0 0
#> [3,] 0 0 0
#> [4,] 0 0 0
#> [5,] 0 0 0
#> ... . . .
#> [8,] 0 0 0
#> [9,] 0 0 0
#> [10,] 0 0 0
#> [11,] 0 0 0
#> [12,] 0 0 0
is(cvg, "DelayedArray") # TRUE
#> [1] TRUE
seed(cvg)
#> An object of class "ReshapedHDF5ArraySeed"
#> Slot "reshaped_dim":
#> [1] 12 90354753
#>
#> Slot "reshaped_chunkdim":
#> [1] 1 88238
#>
#> Slot "filepath":
#> [1] "/usr/local/lib/R/site-library/h5vcData/extdata/example.tally.hfs5"
#>
#> Slot "name":
#> [1] "/ExampleStudy/16/Coverages"
#>
#> Slot "as_sparse":
#> [1] FALSE
#>
#> Slot "type":
#> [1] NA
#>
#> Slot "dim":
#> [1] 6 2 90354753
#>
#> Slot "chunkdim":
#> [1] 1 1 88238
#>
#> Slot "first_val":
#> [1] 0
#>
path(cvg)
#> [1] "/usr/local/lib/R/site-library/h5vcData/extdata/example.tally.hfs5"
dim(cvg)
#> [1] 12 90354753
chunkdim(cvg)
#> [1] 1 88238