Re: [Bioc-devel] inconsistent results from applyPileups and pileLettersAt

[Jesper Gådin]

I am developing packages(if that is of importance), and hoped the thread
could develop into discussions about how to improve the functions
addressed. But can admit that I was not sure where to post this one, as it
definitely is of general concern as well.

Anyway, if anyone found this interesting, here is the post on the support
site :)
https://support.bioconductor.org/p/83141/

On Fri, May 27, 2016 at 5:31 PM, James W. MacDonald  wrote:

> The Bioc-devel list is intended for people who are developing packages.
> Your question should be posted on the bioconductor support site,
> https://support.bioconductor.org.
>
> Jim
>
>
>
> On Fri, May 27, 2016 at 11:05 AM, Jesper Gådin 
> wrote:
>
>> Hello everyone,
>>
>> I find inconsistent results from applyPileups and pileLettersAt. I have a
>> placed a full example on github, so you can try the code with data that
>> will reproduce what I am suspecting is a "bug".
>>
>> #Repo with reproducible example
>> https://github.com/pappewaio/ExampleData
>>
>> #Here a short summary of what is happening
>> One version requires the user to use readGAlignments first and then use
>> pileLettersAt, here I can read in 450 reads into R, but after using
>> pileLettersAt I am left with only 413 counts. What could possibly explain
>> this difference? Is it because some reads are spanning the position I am
>> piling letters at, but not having any sequence information for the
>> position?
>>
>> The second version uses applyPileups and summarize straight from the bam
>> file, and here I would expect to have at least the 413 counts found by
>> pileLettersAt. But instead I can only find 385 counts. Why is it so?
>>
>> Until now I have been using version one to get allele counts. But version
>> two is very much faster, so would be very nice to be able to switch to it,
>> without losing counts.
>>
>> looking forward to hearing your thoughts,
>> Jesper
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>

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Re: [Bioc-devel] inconsistent results from applyPileups and pileLettersAt

[James W. MacDonald]

The Bioc-devel list is intended for people who are developing packages.
Your question should be posted on the bioconductor support site,
https://support.bioconductor.org.

Jim



On Fri, May 27, 2016 at 11:05 AM, Jesper Gådin 
wrote:

> Hello everyone,
>
> I find inconsistent results from applyPileups and pileLettersAt. I have a
> placed a full example on github, so you can try the code with data that
> will reproduce what I am suspecting is a "bug".
>
> #Repo with reproducible example
> https://github.com/pappewaio/ExampleData
>
> #Here a short summary of what is happening
> One version requires the user to use readGAlignments first and then use
> pileLettersAt, here I can read in 450 reads into R, but after using
> pileLettersAt I am left with only 413 counts. What could possibly explain
> this difference? Is it because some reads are spanning the position I am
> piling letters at, but not having any sequence information for the
> position?
>
> The second version uses applyPileups and summarize straight from the bam
> file, and here I would expect to have at least the 413 counts found by
> pileLettersAt. But instead I can only find 385 counts. Why is it so?
>
> Until now I have been using version one to get allele counts. But version
> two is very much faster, so would be very nice to be able to switch to it,
> without losing counts.
>
> looking forward to hearing your thoughts,
> Jesper
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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