The `JaggedArray` class creates a container for storing irregular or jagged array data. This allows the storage of matrices with different dimensions on-disk using HDF5.
Subset a JaggedArray by its interactions ([i,]) or its Hi-C files ([,j]).
`as.list` reads the on-disk data and returns it as an in-memory list of matrices.
Usage
# S4 method for JaggedArray
show(object)
# S4 method for JaggedArray,ANY,ANY,ANY
[(x, i, j, ..., drop = TRUE)
# S4 method for JaggedArray
as.list(x)
# S4 method for JaggedArray
path(object)
# S4 method for JaggedArray
dim(x)Arguments
- object
JaggedArray object.
- x
JaggedArray object.
- i
Numeric vector indicating the indices of interactions to extract.
- j
Numeric vector indicating the indices of files to extract.
- ...
Additional indices for subsetting multidimensional arrays.
- drop
Not accepted for JaggedArray objects.
Value
`JaggedArray()` creates a JaggedArray object.
Subsetting returns a JaggedArray or DelayedArray object (see Details).
`as.list()` returns a list of matrices.
`path()` returns a character vector with the path to the HDF5 file with the JaggedArray data.
`dim()` returns a list of dimensions of the JaggedArray of rows, cols, interactions and files.
Details
NOTE: This class is designed specifically for holding a 4-dimensional JaggedArray <n x m x i x j> where n x m are rows and cols of count matrices, i is interactions, and j is Hi-C files.
The object returned will be a JaggedArray if the submatrices contain different dimensions. However, the returned object will automatically be coerced into a DelayedArray if possible (i.e. the dimensions of the rows and columns are the same.)
The JaggedArray data is still stored on-disk in an HDF5 file until it is coerced into a DelayedArray or realized as a list of matrices.
Slots
h5Filepath to file for creating and storing data as an HDF5 file.
dimdimensions describing the number of matrices contained. dim[1] is the number of interactions, dim[2] is the number of files.
subListis a list of length 2 where the first position refers to interactions and the second refers to files. This list is used to record subsetting operations which are then later applied when accessing data stored in the HDF5 file.
Examples
## Load marinerData
if (!require("marinerData", quietly = TRUE))
BiocManager::install("marinerData")
## Read .hic file paths
hicFiles <- c(
marinerData::LEUK_HEK_PJA27_inter_30.hic(),
marinerData::LEUK_HEK_PJA30_inter_30.hic()
)
#> see ?marinerData and browseVignettes('marinerData') for documentation
#> loading from cache
#> see ?marinerData and browseVignettes('marinerData') for documentation
#> loading from cache
names(hicFiles) <- c("FS", "WT")
## Create test interactions
gi <- read.table(text="
1 51000000 51300000 1 51000000 51500000
2 52000000 52300000 3 52000000 52500000
1 150000000 150500000 1 150000000 150300000
2 52000000 52300000 2 52000000 52800000") |>
as_ginteractions()
## InteractionJaggedArray object
iarr <- pullHicMatrices(gi, hicFiles, 100e03, half="both")
arr <- counts(iarr)
arr
#> <n x m x 4 x 2> JaggedArray:
#> ,,1,1
#> <3 x 5> matrix
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 53 15 5 1 4
#> [2,] 15 68 19 8 5
#> [3,] 5 19 69 12 2
#>
#> ...
#>
#> ,,4,2
#> <3 x 8> matrix
#> [,1] [,2] [,3] ... [,7] [,8]
#> [1,] 31 7 2 . 0 0
#> [2,] 7 22 5 . 1 1
#> [3,] 2 5 26 . 0 2
#>
## Subsetting
arr[,,1,] # DelayedArray
#> <3 x 5 x 1 x 2> DelayedArray object of type "double":
#> ,,1,1
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 53 15 5 1 4
#> [2,] 15 68 19 8 5
#> [3,] 5 19 69 12 2
#>
#> ,,1,2
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 49 27 4 5 3
#> [2,] 27 49 13 2 6
#> [3,] 4 13 56 7 8
#>
arr[,,,1] # JaggedArray
#> <n x m x 4 x 1> JaggedArray:
#> ,,1,1
#> <3 x 5> matrix
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 53 15 5 1 4
#> [2,] 15 68 19 8 5
#> [3,] 5 19 69 12 2
#>
#> ...
#>
#> ,,4,1
#> <3 x 8> matrix
#> [,1] [,2] [,3] ... [,7] [,8]
#> [1,] 29 7 3 . 1 2
#> [2,] 7 28 12 . 0 0
#> [3,] 3 12 29 . 0 1
#>
## Realize as list
as.list(arr)
#> [[1]]
#> [[1]][[1]]
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 53 15 5 1 4
#> [2,] 15 68 19 8 5
#> [3,] 5 19 69 12 2
#>
#> [[1]][[2]]
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 0 0 0
#>
#> [[1]][[3]]
#> [,1] [,2] [,3]
#> [1,] 63 25 15
#> [2,] 25 68 28
#> [3,] 15 28 87
#> [4,] 4 7 45
#> [5,] 2 3 11
#>
#> [[1]][[4]]
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
#> [1,] 29 7 3 3 1 4 1 2
#> [2,] 7 28 12 4 2 3 0 0
#> [3,] 3 12 29 11 3 1 0 1
#>
#>
#> [[2]]
#> [[2]][[1]]
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 49 27 4 5 3
#> [2,] 27 49 13 2 6
#> [3,] 4 13 56 7 8
#>
#> [[2]][[2]]
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] 0 0 0 0 0
#> [2,] 0 0 0 0 0
#> [3,] 0 0 1 0 0
#>
#> [[2]][[3]]
#> [,1] [,2] [,3]
#> [1,] 56 26 8
#> [2,] 26 60 14
#> [3,] 8 14 89
#> [4,] 9 10 22
#> [5,] 2 2 15
#>
#> [[2]][[4]]
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
#> [1,] 31 7 2 2 2 3 0 0
#> [2,] 7 22 5 6 1 2 1 1
#> [3,] 2 5 26 10 4 2 0 2
#>
#>
## Find the data path
path(arr)
#> [1] "/tmp/RtmpwSTrvs/file17dd324eb016.h5"
## Find the data path
dim(arr)
#> $rows
#> [1] 3 3 5 3
#>
#> $cols
#> [1] 5 5 3 8
#>
#> $interactions
#> [1] 4
#>
#> $files
#> [1] 2
#>