[Bioc-devel] Reading and storing single cell ATAC data

Andrew McDavid anmcd at uw.edu
Sat Sep 24 00:46:15 CEST 2016

Hi Caleb,
Hopefully Herve will chime in regarding SummarizedExperiment, but yes, I
think you can and should inherit from that. The `assays` slot must be an
object of type `Assays`, but that does appear to include a sparse Matrix.
See the comments at the top of Assays-class.R in the tarball for
SummarizedExperiment.  For example:

assay=Matrix::Matrix(0, nrow=Nrow, ncol=Ncol, sparse=TRUE)
gr <- GRanges(Rle("chr2", Nrow),
              IRanges(seq_len(Nrow), width=10))
se <- SummarizedExperiment(assays=assay, rowRanges=gr)

As far as out-of-core storage of sparse matrices, I do not know of any good
(portable) solutions.   If it makes more sense to chunk the matrix along
some dimension, you could always pickle the chunked, (sparse) Matrix
objects. In my experience, the decision to adopt sparse vs out-of-core
dense arrays has often required empirical testing to determine what is
fastest/most scalable, since you lose caching benefits from sequential
memory access once you go sparse.  I know there has been talk of extending
SummarizedExperiment to easily permit the Assays to be hdf5-based.

Is disk space really going to be a limiting factor? If so, then you will
probably be IO-bound, so you will need to distribute the data across
computing nodes for your analysis to scale anyways, which suggests some
sort of map-reduce formalism.  Which to my knowledge no one has considered
yet in Bioconductor.  But unless you are generating > 1 TB of
semi-processed data, maybe you don't need to go there?


> Message: 3
> Date: Fri, 23 Sep 2016 17:37:04 -0400
> From: Caleb Lareau <caleblareau at g.harvard.edu>
> To: bioc-devel at r-project.org
> Subject: [Bioc-devel] Reading and storing single cell ATAC data
> Message-ID: <83B8A778-4DAA-4A16-9DA8-22DEF9AD1252 at g.harvard.edu>
> Content-Type: text/plain; charset="UTF-8"
> Hi everyone?
> I?m working with a team that?s generating single cell ATAC data in large
> amounts and am designing the framework of an S4 object to facilitate
> analyses in R. I have a couple of high-level questions that I wanted to
> pose early to hopefully attain some community guidance in the
> implementation of these data structures.
> Question on S4 scATAC Structure--
> It?s easy to imagine scATAC data as a matrix where the rows are particular
> peaks and the columns are individual samples. We already have such an
> impressive volume of data, such that if stored in an ordinary matrix, we
> run into ~20 GB objects. As these data are very sparse, we store the peak
> values in a sparse matrix (through the Matrix library). I wanted to collate
> the peak information (probably in GRanges object) and sample information
> (in a data frame) as well as some potential meta data in an S4 object.
> Easy enough, sure, but after looking at the scRNA structure (e.g. scater <
> https://bioconductor.org/packages/devel/bioc/vignettes/
> scater/inst/doc/vignette.html>), I feel like I should be considering how
> to inherit some of the nice properties from the canonical `ExpressionSet`
> structure. However, since my constraints aren?t directly compatible (namely
> the featureData slot really needs to be a GRanges and the exprs slot must
> be an object from Matrix), it wasn?t clear to me how to maximize the
> inheritance properties while adjusting to my unique constraints. Also, it
> wasn?t clear to me whether or not I could inherent `SummarizedExperiment`
> due to the different nature of the sparse matrix. Does anyone have any
> advice on this structure?
> Question on reading sparse matrices from disk--
> I?m trying to work out the best to selectively read certain rows and
> columns from a sparse matrix on disk into memory. I anticipate a time
> fairly soon that loading our full scATAC data, even in sparse matrices, is
> going to be untenable. Any matrix reading/slicing implementations that I?ve
> seen don?t play friendly with sparse matrices. So, I hacked together two
> solutions? 1) reads and subsets a gzipped matrix with 3 columns (row index;
> column index; non-zero value) through a system call to awk. 2) converts
> that same 3 column matrix into an SQLite object and send queries to read
> values based on indices. The hiccups are that 1) doesn?t play friendly on
> non-unix platforms and always scans the full file, and 2) is faster for
> querying, but the binary object is ~7x larger than the gzipped object. I?ve
> played around with hdf5 as well, but it didn?t seem to give me much back in
> terms of speed or storage benefits comparatively. Has anyone found an
> implementation that achieves a decent!
>   lookup time and compression, or am I essentially needing to choose
> between the two?
> Thanks and have a great weekend!
> -Caleb
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