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

Francesco Napolitano franapoli at gmail.com
Mon Oct 30 11:24:29 CET 2017

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:


  See issues #1, #2, #3 for some discussion about this.

Backend for GDS files:


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)

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,

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