Hi,
I have been using FastqStreamer() and yield() to process a large fastq file in
chunks, modifying both the read and name and then appending the output to a new
fastq file as each chunk is processed. This works great, but would benefit
greatly from being parallelized.
As far as I can tell,
I'd like to do 'data.table-like' subsetting on `S4 class` by using 'i
expression'. However, '[' generic function has the problem to dispatch
S4 method because of its early evaluation of i argument.
e.g.
gslist[Visit == 1, ]
Error in gslist[Visit == 1, ] :
error in evaluating the argument
(copying over to bioc-devel). I do appreciate the very few keystrokes
it takes to do, e.g.
vignette('affy')
of course I can find them all with browseVignettes('affy') and
sometimes the above is not the right name, but I like that the primary
documentation is so close at hand. this is slightly
Hi Ryan,
On 08/05/2014 05:47 PM, Ryan C. Thompson wrote:
Hi again,
I'm looking at the examples in the summarizeOverlaps help page here:
http://www.bioconductor.org/packages/devel/bioc/manuals/GenomicAlignments/man/GenomicAlignments.pdf
And the examples fod preprocess.reads are a little
Mike,
This can be done. I would argue that the convenience your users get from
this is far outweighed by the damage this does to the ability to read and
easily understand the code they are writing. Users, maintainers, etc now
need to know the object class, what columns it has and what variables
The man page '...' section was updated in GenomicAlignments 1.1.24 in
devel. I've now also updated it in 1.0.5 in release.
The '...' does not refer only to the fixed set of args listed below the
dots. The '...' encompasses any argument(s) provided to
summarizeOverlaps() not explicitly stated
Yes, I understand that the ... doesn't only refer to the fixed set of
arguments listed below. I was saying that the *documentation* for the
dots argument in summarizeOverlaps was actually talking about the below
arguments instead. I don't see it documented anywhere that the dots
arguments
Hi Jeff,
See my replies below inline.
On 8/6/14, 7:16 AM, Johnston, Jeffrey wrote:
Hi,
I have been using FastqStreamer() and yield() to process a large fastq file in
chunks, modifying both the read and name and then appending the output to a new
fastq file as each chunk is processed. This
Hi Jeff,
Thanks for the prompt. It looks like bpiterate or bpstream was intended
but didn't quite make it into BiocParallel. I'll discuss with Martin to
see if I'm missing other history / past discussions and then add it in.
Ryan had some ideas for parallel streaming we discussed at Bioc2014
Mike, what about overriding the %in% operator for Gating sets. It keeps
things simple and preserves the existing bracket operator semantics.
Greg
I'd like to do 'data.table-like' subsetting on `S4 class` by using 'i
expression'. However, '[' generic function has the problem to dispatch S4
method
Gebe,
Your suggestion only works in an environment where no formal argument
'i' is defined in any of existing '[' method. e..g
showMethods([)
Function: [ (package base)
x=nonStructure
Once we load the package that exports '[' methods with 'i' (e.g.
'flowCore' ), then method dispatch still
Mike,
This makes sense (I was actually surprised I was able to get my example to
work as easily as I did).
The thing is, if you are dispatching on i (which you must if any methods
do), you HAVE to know what class i is in order to identify the method.
AFAIK there is no way in R of doing that
When reading from an hdf5 file I would like to automatically call a
function I define when datasets of an arbitrary type (see: 'class') are
read from an hdf5 file. Since it looks like the existing infrastructure
(courtesy of the 'callGeneric' parameter in h5read) in rhdf5 was made
for this, I
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