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  1. MuData
  2. NAMESPACE
Browse code

implement writing of anndata-0.8 encoded files (closes #2)

Ilia Kats authored on 08/09/2023 14:18:45
Showing 1 changed files
NAMESPACE
History View file @ 93c42b3
... ... 
@@ -45,11 +45,9 @@ importFrom(methods,setMethod)
45 45 
 importFrom(methods,slot)
46 46 
 importFrom(methods,slotNames)
47 47 
 importFrom(rhdf5,H5Aclose)
48 
-importFrom(rhdf5,H5Acreate)
49 48 
 importFrom(rhdf5,H5Aexists)
50 49 
 importFrom(rhdf5,H5Aopen)
51 50 
 importFrom(rhdf5,H5Aread)
52 
-importFrom(rhdf5,H5Awrite)
53 51 
 importFrom(rhdf5,H5Dclose)
54 52 
 importFrom(rhdf5,H5Dread)
55 53 
 importFrom(rhdf5,H5Fclose)
... ... 
@@ -66,11 +64,7 @@ importFrom(rhdf5,H5Lexists)
66 64 
 importFrom(rhdf5,H5Pclose)
67 65 
 importFrom(rhdf5,H5Pcreate)
68 66 
 importFrom(rhdf5,H5Pset_userblock)
69 
-importFrom(rhdf5,H5Rcreate)
70 67 
 importFrom(rhdf5,H5Rdereference)
71 
-importFrom(rhdf5,H5Sclose)
72 
-importFrom(rhdf5,H5Screate)
73 
-importFrom(rhdf5,H5Tcopy)
74 68 
 importFrom(rhdf5,h5createAttribute)
75 69 
 importFrom(rhdf5,h5createDataset)
76 70 
 importFrom(rhdf5,h5ls)
Browse code

implement reading of AnnData 0.8+ files

Ilia Kats authored on 08/09/2023 11:28:46
Showing 1 changed files
NAMESPACE
History View file @ 6de2ae3
... ... 
@@ -19,6 +19,7 @@ importFrom(MultiAssayExperiment,colData)
19 19 
 importFrom(MultiAssayExperiment,experiments)
20 20 
 importFrom(MultiAssayExperiment,metadata)
21 21 
 importFrom(MultiAssayExperiment,sampleMap)
22 
+importFrom(S4Vectors,DataFrame)
22 23 
 importFrom(S4Vectors,SimpleList)
23 24 
 importFrom(S4Vectors,metadata)
24 25 
 importFrom(SingleCellExperiment,SingleCellExperiment)
Browse code

don't use multiple dispatch, as suggested in https://github.com/Bioconductor/Contributions/issues/2453

Ilia Kats authored on 15/02/2022 12:59:30
Showing 1 changed files
NAMESPACE
History View file @ fa40c4f
... ... 
@@ -2,8 +2,8 @@
2 2
3 3 
 export(readH5AD)
4 4 
 export(readH5MU)
5 
-exportMethods(writeH5AD)
6 
-exportMethods(writeH5MU)
5 
+export(writeH5AD)
6 
+export(writeH5MU)
7 7 
 import(Matrix)
8 8 
 importClassesFrom(DelayedArray,DelayedMatrix)
9 9 
 importClassesFrom(Matrix,Matrix)
Browse code

first implementation of metadata read/write

Ilia Kats authored on 21/12/2021 12:28:26
Showing 1 changed files
NAMESPACE
History View file @ fe9356a
... ... 
@@ -7,6 +7,7 @@ exportMethods(writeH5MU)
7 7 
 import(Matrix)
8 8 
 importClassesFrom(DelayedArray,DelayedMatrix)
9 9 
 importClassesFrom(Matrix,Matrix)
10 
+importClassesFrom(S4Vectors,DataFrame)
10 11 
 importFrom(DelayedArray,BLOCK_write_to_sink)
11 12 
 importFrom(DelayedArray,is_sparse)
12 13 
 importFrom(DelayedArray,start)
... ... 
@@ -16,8 +17,10 @@ importFrom(DelayedArray,write_block)
16 17 
 importFrom(MultiAssayExperiment,MultiAssayExperiment)
17 18 
 importFrom(MultiAssayExperiment,colData)
18 19 
 importFrom(MultiAssayExperiment,experiments)
20 
+importFrom(MultiAssayExperiment,metadata)
19 21 
 importFrom(MultiAssayExperiment,sampleMap)
20 22 
 importFrom(S4Vectors,SimpleList)
23 
+importFrom(S4Vectors,metadata)
21 24 
 importFrom(SingleCellExperiment,SingleCellExperiment)
22 25 
 importFrom(SingleCellExperiment,altExps)
23 26 
 importFrom(SingleCellExperiment,colData)
... ... 
@@ -27,6 +30,7 @@ importFrom(SingleCellExperiment,reducedDims)
27 30 
 importFrom(SingleCellExperiment,rowData)
28 31 
 importFrom(SingleCellExperiment,rowPair)
29 32 
 importFrom(SingleCellExperiment,rowPairNames)
33 
+importFrom(SummarizedExperiment,"metadata<-")
30 34 
 importFrom(SummarizedExperiment,SummarizedExperiment)
31 35 
 importFrom(SummarizedExperiment,assays)
32 36 
 importFrom(SummarizedExperiment,colData)
... ... 
@@ -37,6 +41,8 @@ importFrom(methods,new)
37 41 
 importFrom(methods,setClass)
38 42 
 importFrom(methods,setGeneric)
39 43 
 importFrom(methods,setMethod)
44 
+importFrom(methods,slot)
45 
+importFrom(methods,slotNames)
40 46 
 importFrom(rhdf5,H5Aclose)
41 47 
 importFrom(rhdf5,H5Acreate)
42 48 
 importFrom(rhdf5,H5Aexists)
Browse code

lowercase function names

Ilia Kats authored on 21/12/2021 08:31:53
Showing 1 changed files
NAMESPACE
History View file @ 9e8b2a9
... ... 
@@ -1,9 +1,9 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
-export(ReadH5AD)
4 
-export(ReadH5MU)
5 
-exportMethods(WriteH5AD)
6 
-exportMethods(WriteH5MU)
3 
+export(readH5AD)
4 
+export(readH5MU)
5 
+exportMethods(writeH5AD)
6 
+exportMethods(writeH5MU)
7 7 
 import(Matrix)
8 8 
 importClassesFrom(DelayedArray,DelayedMatrix)
9 9 
 importClassesFrom(Matrix,Matrix)
Browse code

Improve for biocCheck

Danila Bredikhin authored on 15/12/2021 14:53:35
Showing 1 changed files
NAMESPACE
History View file @ 0d832d1
... ... 
@@ -19,6 +19,7 @@ importFrom(MultiAssayExperiment,experiments)
19 19 
 importFrom(MultiAssayExperiment,sampleMap)
20 20 
 importFrom(S4Vectors,SimpleList)
21 21 
 importFrom(SingleCellExperiment,SingleCellExperiment)
22 
+importFrom(SingleCellExperiment,altExps)
22 23 
 importFrom(SingleCellExperiment,colData)
23 24 
 importFrom(SingleCellExperiment,colPair)
24 25 
 importFrom(SingleCellExperiment,colPairNames)
... ... 
@@ -30,6 +31,7 @@ importFrom(SummarizedExperiment,SummarizedExperiment)
30 31 
 importFrom(SummarizedExperiment,assays)
31 32 
 importFrom(SummarizedExperiment,colData)
32 33 
 importFrom(methods,as)
34 
+importFrom(methods,hasMethod)
33 35 
 importFrom(methods,is)
34 36 
 importFrom(methods,new)
35 37 
 importFrom(methods,setClass)
Browse code

Update imports and vignettes

Danila Bredikhin authored on 30/11/2021 01:43:55
Showing 1 changed files
NAMESPACE
History View file @ 1c9dbb0
... ... 
@@ -36,9 +36,11 @@ importFrom(methods,setClass)
36 36 
 importFrom(methods,setGeneric)
37 37 
 importFrom(methods,setMethod)
38 38 
 importFrom(rhdf5,H5Aclose)
39 
+importFrom(rhdf5,H5Acreate)
39 40 
 importFrom(rhdf5,H5Aexists)
40 41 
 importFrom(rhdf5,H5Aopen)
41 42 
 importFrom(rhdf5,H5Aread)
43 
+importFrom(rhdf5,H5Awrite)
42 44 
 importFrom(rhdf5,H5Dclose)
43 45 
 importFrom(rhdf5,H5Dread)
44 46 
 importFrom(rhdf5,H5Fclose)
... ... 
@@ -55,6 +57,11 @@ importFrom(rhdf5,H5Lexists)
55 57 
 importFrom(rhdf5,H5Pclose)
56 58 
 importFrom(rhdf5,H5Pcreate)
57 59 
 importFrom(rhdf5,H5Pset_userblock)
60 
+importFrom(rhdf5,H5Rcreate)
61 
+importFrom(rhdf5,H5Rdereference)
62 
+importFrom(rhdf5,H5Sclose)
63 
+importFrom(rhdf5,H5Screate)
64 
+importFrom(rhdf5,H5Tcopy)
58 65 
 importFrom(rhdf5,h5createAttribute)
59 66 
 importFrom(rhdf5,h5createDataset)
60 67 
 importFrom(rhdf5,h5ls)
Browse code

make R CMD check pass

Ilia Kats authored on 27/09/2021 08:04:15
Showing 1 changed files
NAMESPACE
History View file @ d2dd1d6
... ... 
@@ -29,6 +29,10 @@ importFrom(SingleCellExperiment,rowPairNames)
29 29 
 importFrom(SummarizedExperiment,SummarizedExperiment)
30 30 
 importFrom(SummarizedExperiment,assays)
31 31 
 importFrom(SummarizedExperiment,colData)
32 
+importFrom(methods,as)
33 
+importFrom(methods,is)
34 
+importFrom(methods,new)
35 
+importFrom(methods,setClass)
32 36 
 importFrom(methods,setGeneric)
33 37 
 importFrom(methods,setMethod)
34 38 
 importFrom(rhdf5,H5Aclose)
Browse code

fix writing of DelayedMatrices

Ilia Kats authored on 17/09/2021 09:06:39
Showing 1 changed files
NAMESPACE
History View file @ 3178c43
... ... 
@@ -5,10 +5,30 @@ export(ReadH5MU)
5 5 
 exportMethods(WriteH5AD)
6 6 
 exportMethods(WriteH5MU)
7 7 
 import(Matrix)
8 
+importClassesFrom(DelayedArray,DelayedMatrix)
9 
+importClassesFrom(Matrix,Matrix)
10 
+importFrom(DelayedArray,BLOCK_write_to_sink)
11 
+importFrom(DelayedArray,is_sparse)
12 
+importFrom(DelayedArray,start)
13 
+importFrom(DelayedArray,type)
14 
+importFrom(DelayedArray,width)
15 
+importFrom(DelayedArray,write_block)
8 16 
 importFrom(MultiAssayExperiment,MultiAssayExperiment)
17 
+importFrom(MultiAssayExperiment,colData)
18 
+importFrom(MultiAssayExperiment,experiments)
19 
+importFrom(MultiAssayExperiment,sampleMap)
9 20 
 importFrom(S4Vectors,SimpleList)
10 21 
 importFrom(SingleCellExperiment,SingleCellExperiment)
22 
+importFrom(SingleCellExperiment,colData)
23 
+importFrom(SingleCellExperiment,colPair)
24 
+importFrom(SingleCellExperiment,colPairNames)
25 
+importFrom(SingleCellExperiment,reducedDims)
26 
+importFrom(SingleCellExperiment,rowData)
27 
+importFrom(SingleCellExperiment,rowPair)
28 
+importFrom(SingleCellExperiment,rowPairNames)
11 29 
 importFrom(SummarizedExperiment,SummarizedExperiment)
30 
+importFrom(SummarizedExperiment,assays)
31 
+importFrom(SummarizedExperiment,colData)
12 32 
 importFrom(methods,setGeneric)
13 33 
 importFrom(methods,setMethod)
14 34 
 importFrom(rhdf5,H5Aclose)
... ... 
@@ -38,18 +58,6 @@ importFrom(rhdf5,h5write)
38 58 
 importFrom(rhdf5,h5writeAttribute)
39 59 
 importFrom(rhdf5,h5writeDataset)
40 60 
 importFrom(stats,setNames)
41 
-importMethodsFrom(MultiAssayExperiment,colData)
42 
-importMethodsFrom(MultiAssayExperiment,experiments)
43 
-importMethodsFrom(MultiAssayExperiment,sampleMap)
44 61 
 importMethodsFrom(SingleCellExperiment,"colPair<-")
45 62 
 importMethodsFrom(SingleCellExperiment,"rowPair<-")
46 
-importMethodsFrom(SingleCellExperiment,colData)
47 
-importMethodsFrom(SingleCellExperiment,colPair)
48 
-importMethodsFrom(SingleCellExperiment,colPairNames)
49 
-importMethodsFrom(SingleCellExperiment,reducedDims)
50 
-importMethodsFrom(SingleCellExperiment,rowData)
51 
-importMethodsFrom(SingleCellExperiment,rowPair)
52 
-importMethodsFrom(SingleCellExperiment,rowPairNames)
53 
-importMethodsFrom(SummarizedExperiment,assays)
54 
-importMethodsFrom(SummarizedExperiment,colData)
55 63 
 importMethodsFrom(rhdf5,"&")
Browse code

read/write AnnData layers to different assays of SummarizedExperiment

Ilia Kats authored on 16/09/2021 07:54:49
Showing 1 changed files
NAMESPACE
History View file @ a758786
... ... 
@@ -50,6 +50,6 @@ importMethodsFrom(SingleCellExperiment,reducedDims)
50 50 
 importMethodsFrom(SingleCellExperiment,rowData)
51 51 
 importMethodsFrom(SingleCellExperiment,rowPair)
52 52 
 importMethodsFrom(SingleCellExperiment,rowPairNames)
53 
-importMethodsFrom(SummarizedExperiment,assay)
53 
+importMethodsFrom(SummarizedExperiment,assays)
54 54 
 importMethodsFrom(SummarizedExperiment,colData)
55 55 
 importMethodsFrom(rhdf5,"&")
Browse code

implement read/write of obsp/varp for modalities

Ilia Kats authored on 15/09/2021 15:55:21
Showing 1 changed files
NAMESPACE
History View file @ cd0bc69
... ... 
@@ -41,7 +41,15 @@ importFrom(stats,setNames)
41 41 
 importMethodsFrom(MultiAssayExperiment,colData)
42 42 
 importMethodsFrom(MultiAssayExperiment,experiments)
43 43 
 importMethodsFrom(MultiAssayExperiment,sampleMap)
44 
+importMethodsFrom(SingleCellExperiment,"colPair<-")
45 
+importMethodsFrom(SingleCellExperiment,"rowPair<-")
46 
+importMethodsFrom(SingleCellExperiment,colData)
47 
+importMethodsFrom(SingleCellExperiment,colPair)
48 
+importMethodsFrom(SingleCellExperiment,colPairNames)
44 49 
 importMethodsFrom(SingleCellExperiment,reducedDims)
50 
+importMethodsFrom(SingleCellExperiment,rowData)
51 
+importMethodsFrom(SingleCellExperiment,rowPair)
52 
+importMethodsFrom(SingleCellExperiment,rowPairNames)
45 53 
 importMethodsFrom(SummarizedExperiment,assay)
46 54 
 importMethodsFrom(SummarizedExperiment,colData)
47 55 
 importMethodsFrom(rhdf5,"&")
Browse code

update NAMESPACE

Ilia Kats authored on 15/09/2021 12:45:10
Showing 1 changed files
NAMESPACE
History View file @ dc2aa76
... ... 
@@ -27,6 +27,7 @@ importFrom(rhdf5,H5Gcreate)
27 27 
 importFrom(rhdf5,H5Iget_name)
28 28 
 importFrom(rhdf5,H5Iget_type)
29 29 
 importFrom(rhdf5,H5Iis_valid)
30 
+importFrom(rhdf5,H5Lexists)
30 31 
 importFrom(rhdf5,H5Pclose)
31 32 
 importFrom(rhdf5,H5Pcreate)
32 33 
 importFrom(rhdf5,H5Pset_userblock)
... ... 
@@ -36,6 +37,7 @@ importFrom(rhdf5,h5ls)
36 37 
 importFrom(rhdf5,h5write)
37 38 
 importFrom(rhdf5,h5writeAttribute)
38 39 
 importFrom(rhdf5,h5writeDataset)
40 
+importFrom(stats,setNames)
39 41 
 importMethodsFrom(MultiAssayExperiment,colData)
40 42 
 importMethodsFrom(MultiAssayExperiment,experiments)
41 43 
 importMethodsFrom(MultiAssayExperiment,sampleMap)
Browse code

add some more documentation

Ilia Kats authored on 15/09/2021 09:33:54
Showing 1 changed files
NAMESPACE
History View file @ 57b02c9
... ... 
@@ -8,7 +8,6 @@ import(Matrix)
8 8 
 importFrom(MultiAssayExperiment,MultiAssayExperiment)
9 9 
 importFrom(S4Vectors,SimpleList)
10 10 
 importFrom(SingleCellExperiment,SingleCellExperiment)
11 
-importFrom(SingleCellExperiment,reducedDims)
12 11 
 importFrom(SummarizedExperiment,SummarizedExperiment)
13 12 
 importFrom(methods,setGeneric)
14 13 
 importFrom(methods,setMethod)
Browse code

update NAMESPACE and docs

Ilia Kats authored on 15/09/2021 08:33:07
Showing 1 changed files
NAMESPACE
History View file @ 46e908f
... ... 
@@ -1,11 +1,14 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
+export(ReadH5AD)
3 4 
 export(ReadH5MU)
5 
+exportMethods(WriteH5AD)
4 6 
 exportMethods(WriteH5MU)
5 7 
 import(Matrix)
6 8 
 importFrom(MultiAssayExperiment,MultiAssayExperiment)
7 9 
 importFrom(S4Vectors,SimpleList)
8 10 
 importFrom(SingleCellExperiment,SingleCellExperiment)
11 
+importFrom(SingleCellExperiment,reducedDims)
9 12 
 importFrom(SummarizedExperiment,SummarizedExperiment)
10 13 
 importFrom(methods,setGeneric)
11 14 
 importFrom(methods,setMethod)
... ... 
@@ -28,7 +31,6 @@ importFrom(rhdf5,H5Iis_valid)
28 31 
 importFrom(rhdf5,H5Pclose)
29 32 
 importFrom(rhdf5,H5Pcreate)
30 33 
 importFrom(rhdf5,H5Pset_userblock)
31 
-importFrom(rhdf5,H5iget_type)
32 34 
 importFrom(rhdf5,h5createAttribute)
33 35 
 importFrom(rhdf5,h5createDataset)
34 36 
 importFrom(rhdf5,h5ls)
Browse code

Update DESCRIPTION and NAMESPACE

Danila Bredikhin authored on 14/09/2021 15:30:19
Showing 1 changed files
NAMESPACE
History View file @ e18aff8
... ... 
@@ -24,8 +24,11 @@ importFrom(rhdf5,H5Gclose)
24 24 
 importFrom(rhdf5,H5Gcreate)
25 25 
 importFrom(rhdf5,H5Iget_name)
26 26 
 importFrom(rhdf5,H5Iget_type)
27 
+importFrom(rhdf5,H5Iis_valid)
28 
+importFrom(rhdf5,H5Pclose)
27 29 
 importFrom(rhdf5,H5Pcreate)
28 30 
 importFrom(rhdf5,H5Pset_userblock)
31 
+importFrom(rhdf5,H5iget_type)
29 32 
 importFrom(rhdf5,h5createAttribute)
30 33 
 importFrom(rhdf5,h5createDataset)
31 34 
 importFrom(rhdf5,h5ls)
Browse code

implement file-backed mode with HDF5Array

Ilia Kats authored on 14/09/2021 11:58:38
Showing 1 changed files
NAMESPACE
History View file @ 2b8e115
... ... 
@@ -22,11 +22,14 @@ importFrom(rhdf5,H5Fis_hdf5)
22 22 
 importFrom(rhdf5,H5Fopen)
23 23 
 importFrom(rhdf5,H5Gclose)
24 24 
 importFrom(rhdf5,H5Gcreate)
25 
+importFrom(rhdf5,H5Iget_name)
25 26 
 importFrom(rhdf5,H5Iget_type)
26 27 
 importFrom(rhdf5,H5Pcreate)
27 28 
 importFrom(rhdf5,H5Pset_userblock)
28 29 
 importFrom(rhdf5,h5createAttribute)
30 
+importFrom(rhdf5,h5createDataset)
29 31 
 importFrom(rhdf5,h5ls)
32 
+importFrom(rhdf5,h5write)
30 33 
 importFrom(rhdf5,h5writeAttribute)
31 34 
 importFrom(rhdf5,h5writeDataset)
32 35 
 importMethodsFrom(MultiAssayExperiment,colData)
Browse code

working port to rhdf5

- remove the workaround, it doesn't work. Therefore, this depends on the
rhdf5 version from https://github.com/ilia-kats/rhdf5/tree/attribute-references
- read-write of MultiAssayExperiments works

TODO:
- backed objects with DelayedArray
- figure out how to close all the HDF5 objects when we're done

Ilia Kats authored on 13/09/2021 13:02:50
Showing 1 changed files
NAMESPACE
History View file @ bcce7b1
... ... 
@@ -2,24 +2,37 @@
2 2
3 3 
 export(ReadH5MU)
4 4 
 exportMethods(WriteH5MU)
5 
-import(hdf5r)
6 
-importFrom(Matrix,t)
5 
+import(Matrix)
7 6 
 importFrom(MultiAssayExperiment,MultiAssayExperiment)
7 
+importFrom(S4Vectors,SimpleList)
8 8 
 importFrom(SingleCellExperiment,SingleCellExperiment)
9 9 
 importFrom(SummarizedExperiment,SummarizedExperiment)
10 
+importFrom(methods,setGeneric)
11 
+importFrom(methods,setMethod)
10 12 
 importFrom(rhdf5,H5Aclose)
11 13 
 importFrom(rhdf5,H5Aexists)
12 14 
 importFrom(rhdf5,H5Aopen)
13 15 
 importFrom(rhdf5,H5Aread)
16 
+importFrom(rhdf5,H5Dclose)
14 17 
 importFrom(rhdf5,H5Dread)
15 18 
 importFrom(rhdf5,H5Fclose)
16 19 
 importFrom(rhdf5,H5Fcreate)
17 20 
 importFrom(rhdf5,H5Fget_name)
18 21 
 importFrom(rhdf5,H5Fis_hdf5)
19 22 
 importFrom(rhdf5,H5Fopen)
23 
+importFrom(rhdf5,H5Gclose)
24 
+importFrom(rhdf5,H5Gcreate)
20 25 
 importFrom(rhdf5,H5Iget_type)
21 26 
 importFrom(rhdf5,H5Pcreate)
27 
+importFrom(rhdf5,H5Pset_userblock)
28 
+importFrom(rhdf5,h5createAttribute)
22 29 
 importFrom(rhdf5,h5ls)
23 
-importFrom(rhdf5,h5readAttributes)
24 30 
 importFrom(rhdf5,h5writeAttribute)
25 
-useDynLib(MuData, .registration=TRUE)
31 
+importFrom(rhdf5,h5writeDataset)
32 
+importMethodsFrom(MultiAssayExperiment,colData)
33 
+importMethodsFrom(MultiAssayExperiment,experiments)
34 
+importMethodsFrom(MultiAssayExperiment,sampleMap)
35 
+importMethodsFrom(SingleCellExperiment,reducedDims)
36 
+importMethodsFrom(SummarizedExperiment,assay)
37 
+importMethodsFrom(SummarizedExperiment,colData)
38 
+importMethodsFrom(rhdf5,"&")
Browse code

initial commit

Start port of muon.r MAE functions to rhdf5.
Includes a workaround for missing features in rhdf5. The workaround
works for file creation properties, but not for references, because the
H5Rdereference2 symbol is missing from the rhdf5.so library. This is
because the GNU linker, when linking with a static library, by default
only includes those objects from the static lib that are actually used
in the final output.

Ilia Kats authored on 10/09/2021 14:59:16
Showing 1 changed files
NAMESPACE
History View file @ e8c319b
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,25 @@
1 
+# Generated by roxygen2: do not edit by hand
2 
+
3 
+export(ReadH5MU)
4 
+exportMethods(WriteH5MU)
5 
+import(hdf5r)
6 
+importFrom(Matrix,t)
7 
+importFrom(MultiAssayExperiment,MultiAssayExperiment)
8 
+importFrom(SingleCellExperiment,SingleCellExperiment)
9 
+importFrom(SummarizedExperiment,SummarizedExperiment)
10 
+importFrom(rhdf5,H5Aclose)
11 
+importFrom(rhdf5,H5Aexists)
12 
+importFrom(rhdf5,H5Aopen)
13 
+importFrom(rhdf5,H5Aread)
14 
+importFrom(rhdf5,H5Dread)
15 
+importFrom(rhdf5,H5Fclose)
16 
+importFrom(rhdf5,H5Fcreate)
17 
+importFrom(rhdf5,H5Fget_name)
18 
+importFrom(rhdf5,H5Fis_hdf5)
19 
+importFrom(rhdf5,H5Fopen)
20 
+importFrom(rhdf5,H5Iget_type)
21 
+importFrom(rhdf5,H5Pcreate)
22 
+importFrom(rhdf5,h5ls)
23 
+importFrom(rhdf5,h5readAttributes)
24 
+importFrom(rhdf5,h5writeAttribute)
25 
+useDynLib(MuData, .registration=TRUE)