DelayedArray

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Delayed transposition (`t()` or `aperm()`) significantly slows down block processing of a DelayedMatrix or DelayedArray object. However the result of block-processed operations like `mean()`, `anyNA()`, and members of the "Summary"...

hpages

See https://github.com/MarioniLab/DropletUtils/issues/15 for a discussion about this.

hpages

Would be useful to support subscripting with `NA`s. The rows or columns would just be filled with `NA`.

lawremi

Re-implementing rowsum/colsum for HDF5Matrix

3

I just noticed that **bsseq** has been broken in devel for a while due to the removal of the `rowsum,HDF5Matrix-method` (which I okayed back in https://github.com/Bioconductor/DelayedArray/commit/1a6a44f0119d81ff5eae975a37b4eb4efe85efab#comments). I now remember why...

PeteHaitch

The [_Implementing A DelayedArray Backend_](https://github.com/Bioconductor/DelayedArray/blob/master/vignettes/02-Implementing_a_backend.Rmd) vignette only covers how to implement a backend for read access only. Backends that support saving DelayedArray objects (a.k.a. _realization backends_) are not covered yet....

hpages

possble DelayedArray constructor over `IntegerList` (or other `List`)

3

Hi @hpages , In the `VariantAnnotation` package, the `CollapsedVCF` (or `ExpandedVCF`) are saving the data entries in `IntegerList / CharacterList...`. And in the development of `VCFArray`, we are trying to...

Liubuntu

Adding an mapply-like blockApply() function to the API

2

Hi Hervé, In a recent email you wrote: > At some point the old block-processing functions (i.e. `block_APPLY()`, `block_MAPPLY()`, and `block_APPLY_and_COMBINE()`) will go away. I'd like to request that a...

PeteHaitch

Failed to install geneLenDataBase

5

I tried to install package "geneLenDataBase" to run ChAMP. I kept getting message "Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : namespace 'DelayedArray' 0.24.0 is being loaded, but >=...

fhao2

`base::cbind()`

3

When `x` is an `HDF5Matrix`, but I haven't attached any BioC packages, I get: ```R > cbind(x, x) Error: unable to find an inherited method for function ‘bindCOLS’ for signature...

multimeric

Hi, I ran into a curious edge case, where summing a `ConstantArray` with a vector fails if both are zero and then writing it with HDF5Array::writeHDF5Array, but not in any...

const-ae