Hi Karolis,
These classes have constructor functions of the same name as the class. For
example, the constructor function for GRanges is called GRanges().
If you use the constructors you need to import them separately, e.g.
importFrom GenomicRanges GRanges
Best,
Thomas
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Hi Michael,
ah, I see. I hadn't realized that returning the pileups separately for each
region could be a desired feature, but that makes sense. I agree, as it is
easy for the user to 'reduce' the ranges beforehand your first option (e.g.
returning the ID of the range) would be more flexible.
Per
Hi Michael,
I noticed that when the tallyVariants function receives a 'which' arguments
(via BamTallyParam), that contains overlapping or duplicated regions,
duplicated rows are returned.
(See below for an example.)
It took me a little while to understand where I was picking duplicates.
Would i
Hi Valerie, hi Michael,
I find myself frequently moving back and forth between data.frames, GRanges
and VRanges objects.
The makeGRangesFromDataFrame function from the GenomicRanges makes the
coercion between the former straightforward, but I couldn't find anything
similar for the second step, co
Dear Sebastian,
I noticed a change in behavior of the 'mgsa' method in your 'mgsa' package
between the current release and development versions.
In the release version of R (see sessionInfo below), the following command
works:
mgsa(
o=c("A", "B"),
sets=list(set1 = LETTERS[1:3], set2 = LETT
Hi Herve,
that's brilliant ! Thank you so much for optimizing the method. The new
performance is very impressive.
Cheers,
Thomas
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Hi Herve,
thanks a lot for re-enabling the subsetting functionality for CompressedRleList
with List-like objects.
While things work now, I noticed a big difference in execution time for the
following operations:
with IRanges_1.18.2
rles <- RleList(Rle(values=TRUE,lengths=1),
Hi Herve,
I have updated to IRanges 1.20.4 now, but unfortunately, I still encounter
an error when I try to subset a CompressedRleList or SimpleRleList with
a CompressedIRangesList or SimpleIRangesList.
Would you mind having a look at where I am going wrong ? (My two example
objects are available
Great ! Thanks a ton for addressing this issue so quickly,
Thomas
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extMethod', found a '...' in the matched call, but no
corresponding '...' argument
On Fri, Oct 25, 2013 at 11:23 AM, Thomas Sandmann wrote:
> Dear BioC developers,
>
> I am trying to subset an RleList with an IRangesList (see attached rdata
>
Dear BioC developers,
I am trying to subset an RleList with an IRangesList (see attached rdata
object). Unfortunately, the following line fails with IRanges 1.20.0:
return_rles[keep_ranges] <- TRUE
Error in subsetListByList_replace(x, i, value) :
cannot subscript an unnamed list-like object by
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--
Thomas Sandmann
Computational biologist
Genentech, Inc.
1 DNA Way
South San Francisco, C
Dear Dan,
great, problem solved.
Thanks a lot !
Thomas
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Dear BioC developers,
I upgraded to R 3.0.0 on my Mac (10.6.8) to make my gCMAP package ready for
the next BioC release.
Afterward, I reinstalled all the required BioC packages using biocLite.
My package depends on "org.Hs.eg.db". Unfortunately, installing the latest
"org.Hs.eg.db" via biocLite g
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