Entering edit mode
13 months ago
nadammagdy
▴
10
Hi all,
I am trying to save my Seurat object to h5ad to use it as Anndata, I did it before using MuDataSeurat, with Seurat_4.3.0.1.
`seurat_object = CreateSeuratObject(counts = out, project = 'sample_name')
str(seurat_object)
1st str:
Formal class 'Seurat' [package "SeuratObject"] with 13 slots
..@ assays :List of 1
.. ..$ RNA:Formal class 'Assay' [package "SeuratObject"] with 8 slots
.. .. .. ..@ counts :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
.. .. .. .. .. ..@ i : int [1:5253276] 14 29 38 91 115 124 137 156 197 226 ...
.. .. .. .. .. ..@ p : int [1:4587] 0 1412 2343 3385 4580 5000 5850 7137 8320 9391 ...
.. .. .. .. .. ..@ Dim : int [1:2] 20420 4586
.. .. .. .. .. ..@ Dimnames:List of 2
.. .. .. .. .. .. ..$ : chr [1:20420] "AL627309.1" "AL669831.5" "LINC00115" "FAM41C" ...
.. .. .. .. .. .. ..$ : chr [1:4586] "AAACAGCCACTTAGGC-1" "AAACATGCAACCCTAA-1" "AAACATGCAAGACTCC-1" "AAACATGCACTAAATC-1" ...
.. .. .. .. .. ..@ x : num [1:5253276] 0.934 0.818 0.881 0.798 0.802 ...
.. .. .. .. .. ..@ factors : list()
.. .. .. ..@ data :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
.. .. .. .. .. ..@ i : int [1:5253276] 14 29 38 91 115 124 137 156 197 226 ...
.. .. .. .. .. ..@ p : int [1:4587] 0 1412 2343 3385 4580 5000 5850 7137 8320 9391 ...
.. .. .. .. .. ..@ Dim : int [1:2] 20420 4586
.. .. .. .. .. ..@ Dimnames:List of 2
.. .. .. .. .. .. ..$ : chr [1:20420] "AL627309.1" "AL669831.5" "LINC00115" "FAM41C" ...
.. .. .. .. .. .. ..$ : chr [1:4586] "AAACAGCCACTTAGGC-1" "AAACATGCAACCCTAA-1" "AAACATGCAAGACTCC-1" "AAACATGCACTAAATC-1" ...
.. .. .. .. .. ..@ x : num [1:5253276] 0.934 0.818 0.881 0.798 0.802 ...
.. .. .. .. .. ..@ factors : list()
.. .. .. ..@ scale.data : num[0 , 0 ]
.. .. .. ..@ key : chr "rna_"
.. .. .. ..@ assay.orig : NULL
.. .. .. ..@ var.features : logi(0)
.. .. .. ..@ meta.features:'data.frame': 20420 obs. of 0 variables
.. .. .. ..@ misc : list()
..@ meta.data :'data.frame': 4586 obs. of 3 variables:
.. ..$ orig.ident : Factor w/ 1 level "CS23_F": 1 1 1 1 1 1 1 1 1 1 ...
.. ..$ nCount_RNA : num [1:4586] 2192 1357 1536 1792 751 ...
.. ..$ nFeature_RNA: int [1:4586] 1412 930 1040 1193 420 847 1287 1178 1066 651 ...
..@ active.assay: chr "RNA"
..@ active.ident: Factor w/ 1 level "CS23_F": 1 1 1 1 1 1 1 1 1 1 ...
.. ..- attr(*, "names")= chr [1:4586] "AAACAGCCACTTAGGC-1" "AAACATGCAACCCTAA-1" "AAACATGCAAGACTCC-1" "AAACATGCACTAAATC-1" ...
..@ graphs : list()
..@ neighbors : list()
..@ reductions : list()
..@ images : list()
..@ project.name: chr "CS23_F"
..@ misc : list()
..@ version :Classes 'package_version', 'numeric_version' hidden list of 1
.. ..$ : int [1:3] 4 1 3
..@ commands : list()
..@ tools : list()
'Seurat'
Then with MuDataSeurat::WriteH5AD(seurat_object, "path/seuratobject.h5ad")` I never had problem.
Now when I am using Seurat V5 I get this error with MuDataSeurat.
Error in (function (cl, name, valueClass) :
‘meta.features’ is not a slot in class “Seurat”
I checked the Seurat str and slots are different in the updated version, there is no meta.feature.
2nd str:
Formal class 'Seurat' [package "SeuratObject"] with 13 slots ..@ assays :List of 1 .. ..$ RNA:Formal class 'Assay5' [package "SeuratObject"] with 8 slots .. .. .. ..@ layers :List of 1 .. .. .. .. ..$ counts:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots .. .. .. .. .. .. ..@ i : int [1:14994601] 154 240 493 541 546 567 624 675 684 693 ... .. .. .. .. .. .. ..@ p : int [1:6975] 0 425 1244 1680 5294 7829 10590 13797 15113 15752 ... .. .. .. .. .. .. ..@ Dim : int [1:2] 33538 6974 .. .. .. .. .. .. ..@ Dimnames:List of 2 .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..@ x : num [1:14994601] 0.936 0.985 1.899 0.979 0.973 ... .. .. .. .. .. .. ..@ factors : list() .. .. .. ..@ cells :Formal class 'LogMap' [package "SeuratObject"] with 1 slot .. .. .. .. .. ..@ .Data: logi [1:6974, 1] TRUE TRUE TRUE TRUE TRUE TRUE ... .. .. .. .. .. .. ..- attr(*, "dimnames")=List of 2 .. .. .. .. .. .. .. ..$ : chr [1:6974] "AAACAGCCAACTGGGA-1" "AAACAGCCAAGGTGGC-1" "AAACAGCCACAATGTT-1" "AAACAGCCACTTAGGC-1" ... .. .. .. .. .. .. .. ..$ : chr "counts" .. .. .. .. .. ..$ dim : int [1:2] 6974 1 .. .. .. .. .. ..$ dimnames:List of 2 .. .. .. .. .. .. ..$ : chr [1:6974] "AAACAGCCAACTGGGA-1" "AAACAGCCAAGGTGGC-1" "AAACAGCCACAATGTT-1" "AAACAGCCACTTAGGC-1" ... .. .. .. .. .. .. ..$ : chr "counts" .. .. .. ..@ features :Formal class 'LogMap' [package "SeuratObject"] with 1 slot .. .. .. .. .. ..@ .Data: logi [1:33538, 1] TRUE TRUE TRUE TRUE TRUE TRUE ... .. .. .. .. .. .. ..- attr(*, "dimnames")=List of 2 .. .. .. .. .. .. .. ..$ : chr [1:33538] "MIR1302-2HG" "FAM138A" "OR4F5" "AL627309.1" ... .. .. .. .. .. .. .. ..$ : chr "counts" .. .. .. .. .. ..$ dim : int [1:2] 33538 1 .. .. .. .. .. ..$ dimnames:List of 2 .. .. .. .. .. .. ..$ : chr [1:33538] "MIR1302-2HG" "FAM138A" "OR4F5" "AL627309.1" ... .. .. .. .. .. .. ..$ : chr "counts" .. .. .. ..@ default : int 1 .. .. .. ..@ assay.orig: chr(0) .. .. .. ..@ meta.data :'data.frame': 33538 obs. of 0 variables .. .. .. ..@ misc :List of 1 .. .. .. .. ..$ calcN: logi TRUE .. .. .. ..@ key : chr "rna_" ..@ meta.data :'data.frame': 6974 obs. of 3 variables: .. ..$ orig.ident : Factor w/ 1 level "CS23LV": 1 1 1 1 1 1 1 1 1 1 ... .. ..$ nCount_RNA : num [1:6974] 746 1539 535 8631 5633 ... .. ..$ nFeature_RNA: int [1:6974] 425 818 435 3612 2532 2752 3179 1316 639 2267 ... ..@ active.assay: chr "RNA" ..@ active.ident: Factor w/ 1 level "CS23LV": 1 1 1 1 1 1 1 1 1 1 ... .. ..- attr(*, "names")= chr [1:6974] "AAACAGCCAACTGGGA-1" "AAACAGCCAAGGTGGC-1" "AAACAGCCACAATGTT-1" "AAACAGCCACTTAGGC-1" ... ..@ graphs : list() ..@ neighbors : list() ..@ reductions : list() ..@ images : list() ..@ project.name: chr "CS23LV" ..@ misc : list() ..@ version :Classes 'package_version', 'numeric_version' hidden list of 1 .. ..$ : int [1:3] 5 0 0 ..@ commands : list() ..@ tools : list()
I tried to get the older version again, but I also get the second str of Seurat object each time.
Does anyone know how can I get the first str of Seurat object back or know another way to save it to h5ad?
Thanks
