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

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, Herv? Pag?s 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, Herv?. 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

--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
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