[Bioc-devel] Long-form documentation for DelayedArray?

[Hervé Pagès]

Just to let you know that the process of implementing a DelayedArray
backend is now documented:

 
https://github.com/Bioconductor/DelayedArray/blob/master/vignettes/02-Implementing_a_backend.Rmd

Feedback/questions welcome (preferably as issues on GitHub).

Thanks,
H.


On 10/30/2017 03:27 AM, Francesco Napolitano wrote:
> Oh, I forgot an important point. Does the seed class need to contain
> "Array"? What about "array"? I just remembered that I changed it to
> "array" because I have no "Array" in my namespace.
>
> On Mon, Oct 30, 2017 at 11:24 AM, Francesco Napolitano
> <franapoli at gmail.com> wrote:
>>
>>
>> Il 29/10/2017 22:45, Hervé Pagès ha scritto:
>>
>> In particular, I'd like to read more about how to create a backend for
>> DelayedArray. Is there any documentation available beyond the
>> reference manual?
>>
>>
>> I'm guilty. I plan to remedy this ASAP. In the mean time I'll be glad
>> to help. Note that other people are already working (or planning to
>> work) on other backends:
>>
>> Backend for remote HDF5 data:
>>
>>    https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_vjcitn_RemoteArray&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=9ibHAtmTeiiRRSpiI10_Mz7cTUxXmyzMMIp1Qv4N16M&s=pTtsQDjw-10QQfnx-yqM4Df1dO48NXxq6gQUlPaJfFk&e=
>>
>>    See issues #1, #2, #3 for some discussion about this.
>>
>> Backend for GDS files:
>>
>>    https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_VariantExperiment_issues_1&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=9ibHAtmTeiiRRSpiI10_Mz7cTUxXmyzMMIp1Qv4N16M&s=D7Qo7O5ahMaq4IeBWp7TVD8zwhvhmDrxrlTBz8K4d9g&e=
>>
>>
>> Thank you, Hervé. Maybe I could use some help than! Discussions in issue #2
>> seems useful for my case. I have a specific question: when I create a
>> DelayedArray with my backend, it seems that subset_seed_as_array() is
>> called, which is not really intuitive. Is this normal? What is this first
>> call supposed to do? In my case it fails with dimensionality problems (the
>> array is empty).
>>
>> I did look into HDF5Array code, but I'm not sure I understand what the
>> following is doing:
>>
>> .subset_HDF5ArraySeed_as_array <- function(seed, index)
>> {
>>      ans_dim <- DelayedArray:::get_Nindex_lengths(index, dim(seed))
>>      if (any(ans_dim == 0L)) {
>>          ans <- seed at first_val[0]
>>          dim(ans) <- ans_dim
>>      } else {
>>          ans <- h5read2(seed at file, seed at name, index)
>>      }
>>      ans
>> }
>>
>> In particular, I'm not sure how to interpret the index variable, which seems
>> to be a list. Each element "i" is a vector of indices for the i-th
>> dimension? And what does seed at first_val[0] do? And the first_val attribute
>> in general.
>>
>> Thank you very much for your help,
>> francesco

-- 
Hervé Pagès

Program in Computational Biology
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