Regularize JaggedArray or InteractionJaggedArray objects

InteractionJaggedArray objects and their count matrices (JaggedArray objects) contain variable dimension matrices. The `regularize` function resizes these matrices to the new dimensions supplied in `ndim`. The result is a DelayedArray object (for JaggedArray) or an InteractionArray object (for InteractionJaggedArray).

Usage

regularize(
  x,
  ndim = c(10, 10),
  h5File = tempfile(fileext = ".h5"),
  scale = TRUE,
  nBlocks = 5,
  verbose = TRUE,
  chunkSize = 1,
  compressionLevel = 0,
  ...
)

# S4 method for JaggedArray
regularize(
  x,
  ndim,
  h5File,
  scale,
  nBlocks,
  verbose,
  chunkSize,
  compressionLevel
)

# S4 method for InteractionJaggedArray
regularize(
  x,
  ndim,
  h5File,
  scale,
  nBlocks,
  verbose,
  chunkSize,
  compressionLevel
)

Arguments

x

A JaggedArray or InteractionJaggedArray object.

ndim

Numeric vector of length two describing the new dimensions of the output matrices.

h5File

Character file path to save `.h5` file.

scale

Boolean (TRUE/FALSE) indicating whether the values in the new matrices should be scaled to the total signal in each matrix.

nBlocks

Number of blocks for block-processing JaggedArrays. Default is 5. Increase this for large datasets. To read and process all data at once, set this value to 1.

verbose

Boolean (TRUE or FALSE) describing whether to report block-processing progress.

chunkSize

Number (length one numeric vector) indicating how many values of `x` to chunk for each write to HDF5 stored data. This has downstream implications for accessing subsets later. For small `compressionLevel` values use smaller `chunkSize` values and for large `compressionLevel` values use large (i.e. `length(x)`) values to improve performance.

compressionLevel

Number (length one numeric vector) between 0 (Default) and 9 indicating the compression level used on HDF5 file.

...

Additional arguments.

Value

If `x` is a JaggedArray then `regularize` returns an HDF5-backed 4-dimensional DelayedArray object where the first and second dimensions are the rows and columns of the count matrices (`ndim`), the third dimension is the number of interactions and the fourth dimension is the number of files. If `x` is an InteractionJaggedArray then an InteractionArray object is returned where counts returns the object described above.

Details

Note that the interaction/binSize/count matrices relationship will be inconsistent in the resulting InteractionArray object and the row/col names will not be available.

Examples

## Load marinerData
if (!require("marinerData", quietly = TRUE))
    BiocManager::install("marinerData")

## Read .hic file paths
hicFiles <- c(
    LEUK_HEK_PJA27_inter_30.hic(),
    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()
gi <- c(gi,gi) # make more interactions

## InteractionJaggedArray object
ija <- pullHicMatrices(gi, hicFiles, 100e03, half="both")

## Regularize InteractionJaggedArray
ia <- regularize(ija, ndim=c(5,5), nBlocks=1)
#> / Reading and realizing block 1/1 of file 1/2 ... 
#> OK
#> \ Processing it ... 
#> OK
#> / Reading and realizing block 1/1 of file 2/2 ... 
#> OK
#> \ Processing it ... 
#> OK
aggHicMatrices(ia, nBlocks=1)
#> / reading and realizing block 1/1 ... 
#> ok
#> \ processing it ... 
#> ok
#> <5 x 5> DelayedMatrix object of type "double":
#>           [,1]      [,2]      [,3]      [,4]      [,5]
#> [1,] 1.5333093 0.5283683 0.2446879 0.2068139 0.1215322
#> [2,] 0.9166665 0.8038605 0.5434594 0.3513887 0.1819409
#> [3,] 0.4196802 0.8874755 0.3388203 0.4250340 0.6039009
#> [4,] 0.2658102 0.7882093 1.1711284 0.2252012 0.2712338
#> [5,] 0.1107120 0.7057650 2.0383085 0.1545785 0.1621146

## Regularize JaggedArray
ja <- counts(ija)
regularize(ja, ndim=c(5,5), nBlocks=1)
#> / Reading and realizing block 1/1 of file 1/2 ... 
#> OK
#> \ Processing it ... 
#> OK
#> / Reading and realizing block 1/1 of file 2/2 ... 
#> OK
#> \ Processing it ... 
#> OK
#> <5 x 5 x 8 x 2> HDF5Array object of type "double":
#> ,,1,1
#>             [,1]        [,2]        [,3]        [,4]        [,5]
#> [1,] 0.104433498 0.029556650 0.009852217 0.001970443 0.007881773
#> [2,] 0.066995074 0.081773399 0.023645320 0.008866995 0.008866995
#> [3,] 0.029556650 0.133990148 0.037438424 0.015763547 0.009852217
#> [4,] 0.019704433 0.085714286 0.086699507 0.019704433 0.006896552
#> [5,] 0.009852217 0.037438424 0.135960591 0.023645320 0.003940887
#> 
#> ...
#> 
#> ,,8,2
#>             [,1]        [,2]        [,3]        [,4]        [,5]
#> [1,] 0.203112203 0.021294021 0.013104013 0.014742015 0.000000000
#> [2,] 0.124488124 0.040950041 0.018018018 0.013104013 0.003276003
#> [3,] 0.045864046 0.060606061 0.022932023 0.011466011 0.006552007
#> [4,] 0.029484029 0.098280098 0.034398034 0.010647011 0.009828010
#> [5,] 0.013104013 0.135954136 0.045864046 0.009828010 0.013104013
#>