behalf of Bhagwat,
> Aditya [aditya.bhag...@mpi-bn.mpg.de]
> Sent: Wednesday, September 18, 2019 1:57 PM
> To: Michael Lawrence
> Cc: bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] read_bed()
>
> Hi Michael,
>
> That's a software design dilemma I've encounter
g] on behalf of Bhagwat,
Aditya [aditya.bhag...@mpi-bn.mpg.de]
Sent: Wednesday, September 18, 2019 1:57 PM
To: Michael Lawrence
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] read_bed()
Hi Michael,
That's a software design dilemma I've encountered a few times.
One approach
Lawrence; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] read_bed()
I'm not sure if a function called read_bed() should be plotting or
printing. Is your BED file a known BED variant, i.e., maybe there is a
better name for the file type than "bed"?
On Wed, Sep 18, 2019 at 3:17 A
.@mpi-bn.mpg.de]
> Sent: Wednesday, September 18, 2019 11:31 AM
> To: Michael Lawrence
> Cc: bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] read_bed()
>
> (Typo corrected to avoid confusion)
>
> Michael,
>
> rtracklayer::import.bed() indeed works perfectly for me, so I
-bn.mpg.de]
Sent: Wednesday, September 18, 2019 11:31 AM
To: Michael Lawrence
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] read_bed()
(Typo corrected to avoid confusion)
Michael,
rtracklayer::import.bed() indeed works perfectly for me, so I am dropping
multicrispr::read_bed().
In order to
tember 18, 2019 8:35 AM
To: Michael Lawrence
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] read_bed()
Thank you Michael :-)
Aditya
From: Michael Lawrence [lawrence.mich...@gene.com]
Sent: Tuesday, September 17, 2019 8:49 PM
To: Bhagwat, Aditya
Cc: M
nce
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] read_bed()
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
S
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
r function read_bed, based on data.table::fread is
> doing the job, so I will stick to that .
>
> Thank you for all feedback,
>
> Cheers,
>
> Aditya
>
>
>
> From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Bha
rg] on behalf of Bhagwat,
Aditya [aditya.bhag...@mpi-bn.mpg.de]
Sent: Tuesday, September 17, 2019 2:48 PM
To: Michael Lawrence
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] read_bed()
Oh :-) - Thankyou for explaining!
From: Michael Lawrence [lawrence.
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
o use S4 and whether to mix the two).
>
> Aditya
>
>
> From: Michael Lawrence [lawrence.mich...@gene.com]
> Sent: Tuesday, September 17, 2019 2:23 PM
> To: Bhagwat, Aditya
> Cc: Michael Lawrence; Shepherd, Lori; bioc-devel@r-project.org
> Subject:
From: Michael Lawrence [lawrence.mich...@gene.com]
Sent: Tuesday, September 17, 2019 2:23 PM
To: Bhagwat, Aditya
Cc: Michael Lawrence; Shepherd, Lori; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] read_bed()
The generic documentation does not mention it, but see ?import.bed.
It's similar to
.@gene.com]
> Sent: Tuesday, September 17, 2019 2:05 PM
> To: Bhagwat, Aditya
> Cc: Michael Lawrence; Shepherd, Lori; bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] read_bed()
>
> It breaks it because it's not standard BED; however, using the
> extraCols= argument sho
From: Michael Lawrence [lawrence.mich...@gene.com]
Sent: Tuesday, September 17, 2019 2:05 PM
To: Bhagwat, Aditya
Cc: Michael Lawrence; Shepherd, Lori; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] read_bed()
It breaks it because it's not standard BED; ho
agwat, Aditya
> Cc: Shepherd, Lori; bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] read_bed()
>
> 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 y
...@gene.com]
Sent: Tuesday, September 17, 2019 1:41 PM
To: Bhagwat, Aditya
Cc: Shepherd, Lori; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] read_bed()
I don't see an attachment, nor can I find the multicrispr package
anywhere. The "addressed soon" was referring to the BEDX+Y for
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
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