H5ADMatrixSeed objects

H5ADMatrixSeed is a low-level helper class used to represent a pointer to the central matrix stored of an h5ad file, or to one of the matrices in the /layers group.

It is a virtual class with three concrete subclasses: Dense_H5ADMatrixSeed, CSC_H5ADMatrixSeed, and CSR_H5ADMatrixSeed:

• The Dense_H5ADMatrixSeed class is used when the matrix is stored as a conventional HDF5 dataset in the h5ad file. It is a direct entension of the HDF5ArraySeed class.

• The CSC_H5ADMatrixSeed or CSR_H5ADMatrixSeed classes is used when the matrix is stored in the Compressed Sparse Column or Compressed Sparse Row format in the h5ad file. CSC_H5ADMatrixSeed is a direct entension of CSC_H5SparseMatrixSeed, and CSR_H5ADMatrixSeed a direct entension of CSR_H5SparseMatrixSeed.

Note that an H5ADMatrixSeed derivative is not intended to be used directly. Most end users will typically create and manipulate a higher-level H5ADMatrix object instead. See ?H5ADMatrix for more information.

Usage

## Constructor function:
H5ADMatrixSeed(filepath, layer=NULL)

Arguments

filepath, layer

See ?H5ADMatrix for a description of these arguments.

Details

Dense_H5ADMatrixSeed objects support the same limited set of methods as HDF5ArraySeed objects, and CSC_H5ADMatrixSeed and CSR_H5ADMatrixSeed objects support the same limited set of methods as H5SparseMatrixSeed objects. See ?HDF5ArraySeed and ?H5SparseMatrixSeed for the details.

Value

H5ADMatrixSeed() returns an H5ADMatrixSeed derivative (Dense_H5ADMatrixSeed or CSC_H5ADMatrixSeed or CSR_H5ADMatrixSeed) of shape #variables x #observations.

H5ADMatrixSeed vs H5ADMatrix objects

In order to have access to the full set of operations that are available for DelayedMatrix objects, an H5ADMatrixSeed derivative first needs to be wrapped in a DelayedMatrix object, typically by calling the DelayedArray() constructor on it.

This is what the H5ADMatrix() constructor function does.

Note that the result of this wrapping is an H5ADMatrix object, which is just an H5ADMatrixSeed derivative wrapped in a DelayedMatrix object.

References

https://anndata.readthedocs.io/ for AnnData Python objects and the h5ad format.

See also

• H5ADMatrix objects.

• HDF5ArraySeed and H5SparseMatrixSeed objects.

• readH5AD and writeH5AD in the zellkonverter package for importing/exporting an h5ad file as/from a SingleCellExperiment object.

Examples

library(zellkonverter)
h5ad_file <- system.file("extdata", "krumsiek11.h5ad",
                         package="zellkonverter")
seed <- H5ADMatrixSeed(h5ad_file)
seed
#> An object of class "Dense_H5ADMatrixSeed"
#> Slot "dimnames":
#> [[1]]
#>  [1] "Gata2"  "Gata1"  "Fog1"   "EKLF"   "Fli1"   "SCL"    "Cebpa"  "Pu.1"  
#>  [9] "cJun"   "EgrNab" "Gfi1"  
#> 
#> [[2]]
#>   [1] "0"     "1"     "2"     "3"     "4"     "5"     "6"     "7"     "8"    
#>  [10] "9"     "10"    "11"    "12"    "13"    "14"    "15"    "16"    "17"   
#>  [19] "18"    "19"    "20"    "21"    "22"    "23"    "24"    "25"    "26"   
#>  [28] "27"    "28"    "29"    "30"    "31"    "32"    "33"    "34"    "35"   
#>  [37] "36"    "37"    "38"    "39"    "40"    "41"    "42"    "43"    "44"   
#>  [46] "45"    "46"    "47"    "48"    "49"    "50"    "51"    "52"    "53"   
#>  [55] "54"    "55"    "56"    "57"    "58"    "59"    "60"    "61"    "62"   
#>  [64] "63"    "64"    "65"    "66"    "67"    "68"    "69"    "70"    "71"   
#>  [73] "72"    "73"    "74"    "75"    "76"    "77"    "78"    "79"    "80"   
#>  [82] "81"    "82"    "83"    "84"    "85"    "86"    "87"    "88"    "89"   
#>  [91] "90"    "91"    "92"    "93"    "94"    "95"    "96"    "97"    "98"   
#> [100] "99"    "100"   "101"   "102"   "103"   "104"   "105"   "106"   "107"  
#> [109] "108"   "109"   "110"   "111"   "112"   "113"   "114"   "115"   "116"  
#> [118] "117"   "118"   "119"   "120"   "121"   "122"   "123"   "124"   "125"  
#> [127] "126"   "127"   "128"   "129"   "130"   "131"   "132"   "133"   "134"  
#> [136] "135"   "136"   "137"   "138"   "139"   "140"   "141"   "142"   "143"  
#> [145] "144"   "145"   "146"   "147"   "148"   "149"   "150"   "151"   "152"  
#> [154] "153"   "154"   "155"   "156"   "157"   "158"   "159"   "0-1"   "1-1"  
#> [163] "2-1"   "3-1"   "4-1"   "5-1"   "6-1"   "7-1"   "8-1"   "9-1"   "10-1" 
#> [172] "11-1"  "12-1"  "13-1"  "14-1"  "15-1"  "16-1"  "17-1"  "18-1"  "19-1" 
#> [181] "20-1"  "21-1"  "22-1"  "23-1"  "24-1"  "25-1"  "26-1"  "27-1"  "28-1" 
#> [190] "29-1"  "30-1"  "31-1"  "32-1"  "33-1"  "34-1"  "35-1"  "36-1"  "37-1" 
#> [199] "38-1"  "39-1"  "40-1"  "41-1"  "42-1"  "43-1"  "44-1"  "45-1"  "46-1" 
#> [208] "47-1"  "48-1"  "49-1"  "50-1"  "51-1"  "52-1"  "53-1"  "54-1"  "55-1" 
#> [217] "56-1"  "57-1"  "58-1"  "59-1"  "60-1"  "61-1"  "62-1"  "63-1"  "64-1" 
#> [226] "65-1"  "66-1"  "67-1"  "68-1"  "69-1"  "70-1"  "71-1"  "72-1"  "73-1" 
#> [235] "74-1"  "75-1"  "76-1"  "77-1"  "78-1"  "79-1"  "80-1"  "81-1"  "82-1" 
#> [244] "83-1"  "84-1"  "85-1"  "86-1"  "87-1"  "88-1"  "89-1"  "90-1"  "91-1" 
#> [253] "92-1"  "93-1"  "94-1"  "95-1"  "96-1"  "97-1"  "98-1"  "99-1"  "100-1"
#> [262] "101-1" "102-1" "103-1" "104-1" "105-1" "106-1" "107-1" "108-1" "109-1"
#> [271] "110-1" "111-1" "112-1" "113-1" "114-1" "115-1" "116-1" "117-1" "118-1"
#> [280] "119-1" "120-1" "121-1" "122-1" "123-1" "124-1" "125-1" "126-1" "127-1"
#> [289] "128-1" "129-1" "130-1" "131-1" "132-1" "133-1" "134-1" "135-1" "136-1"
#> [298] "137-1" "138-1" "139-1" "140-1" "141-1" "142-1" "143-1" "144-1" "145-1"
#> [307] "146-1" "147-1" "148-1" "149-1" "150-1" "151-1" "152-1" "153-1" "154-1"
#> [316] "155-1" "156-1" "157-1" "158-1" "159-1" "0-2"   "1-2"   "2-2"   "3-2"  
#> [325] "4-2"   "5-2"   "6-2"   "7-2"   "8-2"   "9-2"   "10-2"  "11-2"  "12-2" 
#> [334] "13-2"  "14-2"  "15-2"  "16-2"  "17-2"  "18-2"  "19-2"  "20-2"  "21-2" 
#> [343] "22-2"  "23-2"  "24-2"  "25-2"  "26-2"  "27-2"  "28-2"  "29-2"  "30-2" 
#> [352] "31-2"  "32-2"  "33-2"  "34-2"  "35-2"  "36-2"  "37-2"  "38-2"  "39-2" 
#> [361] "40-2"  "41-2"  "42-2"  "43-2"  "44-2"  "45-2"  "46-2"  "47-2"  "48-2" 
#> [370] "49-2"  "50-2"  "51-2"  "52-2"  "53-2"  "54-2"  "55-2"  "56-2"  "57-2" 
#> [379] "58-2"  "59-2"  "60-2"  "61-2"  "62-2"  "63-2"  "64-2"  "65-2"  "66-2" 
#> [388] "67-2"  "68-2"  "69-2"  "70-2"  "71-2"  "72-2"  "73-2"  "74-2"  "75-2" 
#> [397] "76-2"  "77-2"  "78-2"  "79-2"  "80-2"  "81-2"  "82-2"  "83-2"  "84-2" 
#> [406] "85-2"  "86-2"  "87-2"  "88-2"  "89-2"  "90-2"  "91-2"  "92-2"  "93-2" 
#> [415] "94-2"  "95-2"  "96-2"  "97-2"  "98-2"  "99-2"  "100-2" "101-2" "102-2"
#> [424] "103-2" "104-2" "105-2" "106-2" "107-2" "108-2" "109-2" "110-2" "111-2"
#> [433] "112-2" "113-2" "114-2" "115-2" "116-2" "117-2" "118-2" "119-2" "120-2"
#> [442] "121-2" "122-2" "123-2" "124-2" "125-2" "126-2" "127-2" "128-2" "129-2"
#> [451] "130-2" "131-2" "132-2" "133-2" "134-2" "135-2" "136-2" "137-2" "138-2"
#> [460] "139-2" "140-2" "141-2" "142-2" "143-2" "144-2" "145-2" "146-2" "147-2"
#> [469] "148-2" "149-2" "150-2" "151-2" "152-2" "153-2" "154-2" "155-2" "156-2"
#> [478] "157-2" "158-2" "159-2" "0-3"   "1-3"   "2-3"   "3-3"   "4-3"   "5-3"  
#> [487] "6-3"   "7-3"   "8-3"   "9-3"   "10-3"  "11-3"  "12-3"  "13-3"  "14-3" 
#> [496] "15-3"  "16-3"  "17-3"  "18-3"  "19-3"  "20-3"  "21-3"  "22-3"  "23-3" 
#> [505] "24-3"  "25-3"  "26-3"  "27-3"  "28-3"  "29-3"  "30-3"  "31-3"  "32-3" 
#> [514] "33-3"  "34-3"  "35-3"  "36-3"  "37-3"  "38-3"  "39-3"  "40-3"  "41-3" 
#> [523] "42-3"  "43-3"  "44-3"  "45-3"  "46-3"  "47-3"  "48-3"  "49-3"  "50-3" 
#> [532] "51-3"  "52-3"  "53-3"  "54-3"  "55-3"  "56-3"  "57-3"  "58-3"  "59-3" 
#> [541] "60-3"  "61-3"  "62-3"  "63-3"  "64-3"  "65-3"  "66-3"  "67-3"  "68-3" 
#> [550] "69-3"  "70-3"  "71-3"  "72-3"  "73-3"  "74-3"  "75-3"  "76-3"  "77-3" 
#> [559] "78-3"  "79-3"  "80-3"  "81-3"  "82-3"  "83-3"  "84-3"  "85-3"  "86-3" 
#> [568] "87-3"  "88-3"  "89-3"  "90-3"  "91-3"  "92-3"  "93-3"  "94-3"  "95-3" 
#> [577] "96-3"  "97-3"  "98-3"  "99-3"  "100-3" "101-3" "102-3" "103-3" "104-3"
#> [586] "105-3" "106-3" "107-3" "108-3" "109-3" "110-3" "111-3" "112-3" "113-3"
#> [595] "114-3" "115-3" "116-3" "117-3" "118-3" "119-3" "120-3" "121-3" "122-3"
#> [604] "123-3" "124-3" "125-3" "126-3" "127-3" "128-3" "129-3" "130-3" "131-3"
#> [613] "132-3" "133-3" "134-3" "135-3" "136-3" "137-3" "138-3" "139-3" "140-3"
#> [622] "141-3" "142-3" "143-3" "144-3" "145-3" "146-3" "147-3" "148-3" "149-3"
#> [631] "150-3" "151-3" "152-3" "153-3" "154-3" "155-3" "156-3" "157-3" "158-3"
#> [640] "159-3"
#> 
#> 
#> Slot "filepath":
#> [1] "/usr/local/lib/R/site-library/zellkonverter/extdata/krumsiek11.h5ad"
#> 
#> Slot "name":
#> [1] "/X"
#> 
#> Slot "as_sparse":
#> [1] FALSE
#> 
#> Slot "type":
#> [1] NA
#> 
#> Slot "dim":
#> [1]  11 640
#> 
#> Slot "chunkdim":
#> NULL
#> 
#> Slot "first_val":
#> [1] 0.8032
#> 
path(seed)
#> [1] "/usr/local/lib/R/site-library/zellkonverter/extdata/krumsiek11.h5ad"
dim(seed)
#> [1]  11 640
is_sparse(seed)
#> [1] FALSE

DelayedArray(seed)
#> <11 x 640> H5ADMatrix object of type "double":
#>              0       1       2 ...   158-3   159-3
#> Gata2   0.8032  0.7239  0.6578   .  0.0063  0.0049
#> Gata1  -0.0005  0.0016  0.0013   . -0.0023  0.0002
#> Fog1   -0.0001 -0.0003 -0.0010   . -0.0005 -0.0013
#> EKLF    0.0003 -0.0010 -0.0027   .  0.0081  0.0054
#> Fli1    0.0013  0.0011  0.0025   . -0.0046 -0.0036
#> SCL     0.0011  0.0022  0.0011   . -0.0006  0.0009
#> Cebpa   0.7997  0.8195  0.8358   .  0.9983  1.0011
#> Pu.1    0.8017  0.7256  0.6624   .  0.9970  0.9967
#> cJun    0.0006  0.0784  0.1105   .  0.0109  0.0066
#> EgrNab  0.0009  0.0077  0.0239   . -0.0030 -0.0033
#> Gfi1    0.0002  0.0941  0.1497   .  0.9118  0.9177
stopifnot(class(DelayedArray(seed)) == "H5ADMatrix")