Hi all,
I recently asked about ways to do non-standard read counting in
summarizeOverlaps, and Martin Morgan directed me toward writing a custom
function to pass as the "mode" parameter. I have now written the custom
modes that I require for counting my ChIP-Seq reads, and I figured I
would c
Hi Ryan,
These sound like great contributions. I didn't get an attachment - did
you send one?
Thanks.
Valerie
On 04/30/2014 01:06 PM, Ryan C. Thompson wrote:
Hi all,
I recently asked about ways to do non-standard read counting in
summarizeOverlaps, and Martin Morgan directed me toward writi
No, I forgot to attach the file. Here is the link:
https://www.dropbox.com/s/7qghtksl3mbvlsl/counting-modes.R
On Wed 30 Apr 2014 02:18:28 PM PDT, Valerie Obenchain wrote:
Hi Ryan,
These sound like great contributions. I didn't get an attachment - did
you send one?
Thanks.
Valerie
On 04/30/20
Thanks.
I have some concerns about the *ExtraArgs() functions. Passing flexible
args to findOverlaps in the existing mode functions fundamentally
changes the documented behavior. The modes were created to capture
specific overlap situations pertaining to gene features which are
graphically de
Hi Valerie,
On Thu May 1 13:27:16 2014, Valerie Obenchain wrote:
I have some concerns about the *ExtraArgs() functions. Passing
flexible args to findOverlaps in the existing mode functions
fundamentally changes the documented behavior. The modes were created
to capture specific overlap situatio
On 05/01/2014 02:05 PM, Ryan wrote:
Hi Valerie,
On Thu May 1 13:27:16 2014, Valerie Obenchain wrote:
I have some concerns about the *ExtraArgs() functions. Passing
flexible args to findOverlaps in the existing mode functions
fundamentally changes the documented behavior. The modes were created
GenomicAlignments 1.1.8 has a 'preprocess.reads' argument. This should
be a function where the first argument is 'reads' and the return value
is compatible with 'reads' in the pre-defined count modes.
I've used your ResizeReads() as an example in the man page. I think the
ability to pre-filter
Hi Valerie,
I got really busy around May and never got a chance to thank you for
adding this option to summarizeOverlaps! So thank you!
-Ryan
On Thu 01 May 2014 04:25:33 PM PDT, Valerie Obenchain wrote:
GenomicAlignments 1.1.8 has a 'preprocess.reads' argument. This should
be a function wher
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 confusing. One of
the examples passes some additional "..." opt
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 confus
Ok, I had a look at the code, and I think understand now. The help text
for the "..." argument says "Additional arguments for BAM file methods
such assingleEnd,fragmentsorparamthat apply to the reading of records
from a file (see below)." But this is actually referring to the fixed
set of indiv
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 i
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 pas
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