Hi guys,
Agreed. This is addressed in IRanges 2.1.40. Now you get a warning:
> Views(RleList(b=21:24, a=11:16), RangesList(a=IRanges(2:3, 6),
b=IRanges(1, 4)))
RleViewsList of length 2
names(2): a b
Warning message:
In RleViewsList(rleList = subject, rangesList = start) :
'rleLi
Hmm. I guess we could do at least two things:
1) Return the ID of the which range for each variant, like readVcf does
with its paramRangeID column in the rowData.
2) Do as you suggest, and reduce() the which.
Obviously, these address different use cases. The user can always achieve
#2 by just re
Hi guys,
On 02/20/2015 04:17 PM, Michael Lawrence wrote:
On Thu, Feb 19, 2015 at 12:46 PM, Thomas Sandmann
wrote:
Hi Valerie, hi Michael,
I find myself frequently moving back and forth between data.frames,
GRanges and VRanges objects.
The makeGRangesFromDataFrame function from the GenomicRa
On Thu, Feb 19, 2015 at 12:46 PM, Thomas Sandmann
wrote:
> 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 straig
Hi Thomas,
I've added support for direct access to an arbitrary subset of sequences
in FASTA files. It works in 3 steps:
Step 1: Call fasta.index() to get an index of what's in your files:
library(Biostrings)
filepaths <- c(path1, path2, path3, etc...)
fai <- fasta.index(filepaths,
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
Clearly the Views method has to handle that, and in my opinion return it in
the order of cds list in this case. Anything else is way too fragile.
On Fri, Feb 20, 2015 at 8:14 AM, Sean Davis wrote:
> On Fri, Feb 20, 2015 at 8:10 AM, Malcolm Perry
> wrote:
>
> > Hi Sean,
> >
> > The idiom I've m
Thanks so much for your comments and help!
Best,
Dongmei
From: Gabe Becker [mailto:becker.g...@gene.com]
Sent: Friday, February 20, 2015 9:33 AM
To: Li, Dongmei
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] A quick questions on writing R functions
Dongmei,
This isn't really the right l
Dongmei,
This isn't really the right list for this type of question. That said, I
can give you a few pointers.
The actual section of the manual you quoted is about documenting your
function, not the code of the function itself.
That said, "eval" is not a good name for your function. It doesn't t
Thanks so much for your help!
Best,
Dongmei
-Original Message-
From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf Of Elena
Grassi
Sent: Friday, February 20, 2015 9:21 AM
To: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] A quick questions on writing R functions
I w
I would guess that you need to add to the man page of the function in
the value section something like:
A named list with the following components:
\itemize{
\item \code{"p_pvalue"}: description of p_pvalue
\item \code{"p_tstat"}: description of p_tstat
}
HTH,
E.
--
$ pom
__
Hi,
I'm developing an R package and got the following suggestions for revising the
functions:
"When a function returns a named list, a good practise is to start the
\value section with the following:
A named list with the following components:
and then to itemize the components"
This
On Fri, Feb 20, 2015 at 8:10 AM, Malcolm Perry wrote:
> Hi Sean,
>
> The idiom I've most often seen for getting round this problem is to first
> find matching chromosomes in the RleList, and subset the RangesList based
> on this order:
>
> chrs = intersect(names(rle_list), as.character(seqlevels(
Hi Sean,
The idiom I've most often seen for getting round this problem is to first
find matching chromosomes in the RleList, and subset the RangesList based
on this order:
chrs = intersect(names(rle_list), as.character(seqlevels(windows)))
myViews = Views(rle_list[chrs], as(windows, "RangesList")
I am calculating coverage metrics of a BAM file on the CDS regions. When I
form the RangesList and do coverage(), the resulting coverage vector
applies the views to the regions from the RangesList without checking on
matching ordering or seqlevels of the RleList and the RangesList. This
results,
Hello,
In the previous Bioconductor release (2.14), a countData object from the
baySeq package could be accessed by sample names. Now it seems that it
can be accessed only by indices (version 2.0.50). Was this done on
purpose or is it a bug unnoticed so far? I discovered this as baySeq
fails w
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