[Bioc-devel] Convertion of DataFrame with XStringSets to data.frame

[Hervé Pagès]

Hi Julian, Michael,

On 05/02/2014 04:58 AM, Michael Lawrence wrote:
> This looks like it is due to the changes to as.data.frame,List. XStringSet
> just needs a method that preserves the original behavior.

Just added to Biostrings 2.33.6. Thanks for the catch!

H.

>
>
> On Fri, May 2, 2014 at 1:54 AM, Julian Gehring <julian.gehring at embl.de>wrote:
>
>> Hi,
>>
>> With the latest bioc-devel, the convertion of XStringSets within a
>> DataFrame to a data.frame behaves strangely:
>>
>>    library(Biostrings)
>>    dss = DNAStringSet(c("ACT", "AAA"))
>>    DF = DataFrame(dss)
>>
>>    as(DF, "data.frame")
>>
>> In the latest bioc-devel, this splits the strings:
>>
>>    dss.group dss.group_name dss.value
>> 1         1           <NA>         A
>> 2         1           <NA>         C
>> 3         1           <NA>         T
>> 4         2           <NA>         A
>> 5         2           <NA>         A
>> 6         2           <NA>         A
>>
>> In older versions of bioc-devel (e.g. from last week) and bioc-stable,
>> this keeps the structure and converts to strings to factor levels:
>>
>>    dss
>> 1 ACT
>> 2 AAA
>>
>> Any idea what is causing this?
>>
>> Best wishes
>> Julian
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
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-- 
Hervé Pagès

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