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ReshapedHDF5ArraySeed objects

ReshapedHDF5ArraySeed-class.Rd

ReshapedHDF5ArraySeed is a low-level helper class for representing a pointer to a virtually reshaped HDF5 dataset.

ReshapedHDF5ArraySeed objects are not intended to be used directly. Most end users should create and manipulate ReshapedHDF5Array objects instead. See ?ReshapedHDF5Array for more information.

Usage

## Constructor function:
ReshapedHDF5ArraySeed(filepath, name, dim, type=NA)

Arguments

filepath, name, dim, type

See ?ReshapedHDF5Array for a description of these arguments.

Details

No operation can be performed directly on a ReshapedHDF5ArraySeed object. It first needs to be wrapped in a DelayedArray object. The result of this wrapping is a ReshapedHDF5Array object (a ReshapedHDF5Array object is just a ReshapedHDF5ArraySeed object wrapped in a DelayedArray object).

Value

A ReshapedHDF5ArraySeed object.

See also

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

## Collapse the first 2 dimensions:
seed <- ReshapedHDF5ArraySeed(tally_file, "/ExampleStudy/16/Coverages",
                              dim=c(12, 90354753))
seed
#> 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(seed)
#> [1] "/usr/local/lib/R/site-library/h5vcData/extdata/example.tally.hfs5"
dim(seed)
#> [1]       12 90354753
chunkdim(seed)
#> [1]     1 88238