Thank you Michael :-)
Aditya
From: Michael Lawrence [lawrence.mich...@gene.com]
Sent: Tuesday, September 17, 2019 8:49 PM
To: Bhagwat, Aditya
Cc: Michael Lawrence; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] read_bed()
I think you probably made a mi
Hi,
I'm happy to report that this was never a connection issue. I was just
mislead by
https://stackoverflow.com/questions/25487593/r-what-does-incomplete-block-on-file-mean
which suggested that the download was incomplete as well as the timing
of the connection issue with the non-bioc website. It
I think you probably made a mistake when dropping the columns. When I
provide the extraCols= argument (inventing my own names for things),
it almost works, but it breaks due to NAs in the extra columns. The
"." character is the standard way to express NA in BED files. I've
added support for extra
Thanks Ashish for the quick fix.
For the record the change to tidyr::gather() in the latest version of
tidyr (v 1.0.0) also breaks the CNPBayes and SummarizedBenchmark packages:
https://bioconductor.org/checkResults/3.9/bioc-LATEST/CNPBayes/malbec2-buildsrc.html
https://bioconductor.org/che
Hi Paul,
We have firefox on the Linux builders:
> getOption("browser")
[1] "/usr/bin/firefox"
> browseURL("https://www.bioconductor.org/packages/igvR";)
However it could be that this works, not because firefox somehow gets
started in headless mode, but because we have Xvfb (X11 virtual frame
Hi Lori,
Thank you for your help. I was able to reproduce the issue locally after
updating the packages. I updated the vignette with the changes and pushed
it on both RELEASE_3_9 and the development (3_10) branches. Again thank you
for your help!
Regards,
Ashish Jain
On Tue, Sep 17, 2019 at 7:06
Hi Michael,
I removed the additional metadata columns in SRF.bed
https://gitlab.gwdg.de/loosolab/software/multicrispr/blob/master/inst/extdata/SRF.bed
But still can't get rtracklayer::import.bed working:
> rtracklayer::import.bed(bedfile)
Error in scan(file = file, what = what, sep = sep, quote
I just came across this issue on rmarkdown which links the same problem
to BiocStyle.
The post is from Nov 2017.
https://github.com/rstudio/rmarkdown/issues/1207
Maybe this helps to understand the underlying problem?
It was suggested to check this in BiocStyle:
Have you reported to the authors
Hey Bioc-devel community,
My package OUTRIDER fails again sometimes on the build system but rather
randomly. First I thought it was due to the ImageMagick problem I posted
some days ago. But this is really only a warning.
I guess I found the problem. But this I dont really understand. Any help
is
On Sep 12, 2019, at 3:13 PM, Pages, Herve wrote:
>
> AFAIK the build machines have web browsers.
Hi Herve,
I’d like to do my local linux testing of igvR using the same web browser you
have on the bioc linux build machines.I’d be grateful if you could tell me
which one is installed.
Thank
Oh :-) - Thankyou for explaining!
From: Michael Lawrence [lawrence.mich...@gene.com]
Sent: Tuesday, September 17, 2019 2:40 PM
To: Bhagwat, Aditya
Cc: Michael Lawrence; Shepherd, Lori; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] read_bed()
Having a "
Having a "." in the function name does not make something "S3".
There's no dispatch from import() to import.bed(). Had I not been a
total newb when I created rtracklayer, I would have called the
function importBed() or something like that. Sorry for the confusion.
On Tue, Sep 17, 2019 at 5:34 AM B
Oh, superb, thx!
Interesting ... here you use S3 rather than S4 - I wonder the design intention
underlying these choices (I'm asking because I am trying to figure out myself
when to use S3 and when to use S4 and whether to mix the two).
Aditya
From: Mic
The generic documentation does not mention it, but see ?import.bed.
It's similar to colClasses on read.table().
On Tue, Sep 17, 2019 at 5:15 AM Bhagwat, Aditya
wrote:
>
> Thankyou Michael,
>
> How do I use the extraCols argument? The documentation does not mention an
> `extraCols` argument expli
Thankyou Michael,
How do I use the extraCols argument? The documentation does not mention an
`extraCols` argument explicitly, so it must be one of the ellipsis arguments,
but `?rtracklayer::import` does not mention it. Should I say extraCols = 10
(ten extra columns) or so?
Aditya
___
It breaks it because it's not standard BED; however, using the
extraCols= argument should work in this case. Requiring an explicit
format specification is intentional, because it provides validation
and type safety, and it communicates the format to a future reader.
This also looks a bit like a bed
Hi Michael,
Yeah, I also noticed that the attachment was eaten when it entered the
bio-devel list.
The file is also accessible in the extdata of the multicrispr:
https://gitlab.gwdg.de/loosolab/software/multicrispr/blob/master/inst/extdata/SRF.bed
A bedfile to GRanges importer requires columns
I am able to reproduce the ERROR. It seems to be an issue of trying to subset.
> head(exp %>% gather(Tissue))
Tissue value
1 Adipose Tissue 1.63226821549951
2 Adipose Tissue 0
3 Adipose Tissue 0
4 Adipose Tissue 0.485426827170242
5 Adipose Ti
I don't see an attachment, nor can I find the multicrispr package
anywhere. The "addressed soon" was referring to the BEDX+Y formats,
which was addressed many years ago, so I've updated the documentation.
Broken BED files will never be supported.
Michael
On Tue, Sep 17, 2019 at 4:17 AM Bhagwat, A
Hi Lori,
I remember now - I tried this function earlier, but it does not work for my
bedfiles, like the one in attach.
> bedfile <- system.file('extdata/SRF.bed', package = 'multicrispr')
>
> targetranges <- rtracklayer::import(bedfile, format = 'BED', genome = 'mm10')
Error in scan(file =
Aha - thx!
Aditya
From: Shepherd, Lori [lori.sheph...@roswellpark.org]
Sent: Tuesday, September 17, 2019 1:02 PM
To: Bhagwat, Aditya; bioc-devel@r-project.org
Subject: Re: read_bed()
Please look at rtracklayer::import() function that we recommend for reading of
Please look at rtracklayer::import() function that we recommend for reading of
BAM files along with other common formats.
Cheers,
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
Dear bioc-devel,
I had two feedback requests regarding the function read_bed().
1) Did I overlook, and therefore, re-invent existing functionality?
2) If not, would `read_bed` be suited for existence in a more foundational
package, e.g. `GenomicRanges`, given the rather basal nature of this
fun
Owkies, will file a PR in one of the coming days. And continue the discussion
when I do so.
Cheers!
Aditya
From: Stuart Lee [le...@wehi.edu.au]
Sent: Tuesday, September 17, 2019 5:33 AM
To: Michael Lawrence
Cc: Bhagwat, Aditya; bioc-devel@r-project.org
Subject:
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