Subset

[gewirtz]

Hi, I'm having an issue with subset when I try to subset a loom object with layers. For example:

Edit: I'm using the loomR dev branch of Seurat for NormalizeData

test <- connect(filename = "test.loom", mode="r+")

test Class: loom Filename: test.loom Access type: H5F_ACC_RDWR Attributes: CreationDate, LOOM_SPEC_VERSION, version, last_modified Listing: name obj_type dataset.dims dataset.type_class col_attrs H5I_GROUP <NA> <NA> col_graphs H5I_GROUP <NA> <NA> layers H5I_GROUP <NA> <NA> matrix H5I_DATASET 9602 x 33593 H5T_FLOAT row_attrs H5I_GROUP <NA> <NA> row_graphs H5I_GROUP <NA> <NA>

This works fine: test2 <- subset(test, m= which(!(test$col.attrs$filtered_out[])), filename = "test2.loom")

but this doesn't: NormalizeData(object = test2, chunk.size = 1000, scale.factor = 10000, display.progress = FALSE) test3 <- subset(test2, n=which(test2[["row_attrs/ex_attr"]][]>1), filename="test3.loom")

yielding: Error in [[.H5File(new.loom, "layers") : An object with name layers does not exist in this group

Thanks!!

[mojaveazure]

Thanks for reporting. This should be fixed as of 8e0f54f