[BioC] NucleR: processReads/solveUserSEW0 - Error

[Martin Morgan]

On 11/03/2011 06:14 AM, Oscar Flores wrote:
> So this error happens here, no?
>
> res = RangedData(IRanges(start=position(ar),width=width(ar)),
> strand=strand(ar),space=ar at chromosome)

better to use the accessor chromosome(ar). The error

 > Fehler in solveUserSEW0(start = start, end = end, width = width) :
 > solving row 16512893: range cannot be determined from the supplied
 > arguments (too many NAs)

suggests that position(ar)[16512893] and / or width(ar)[16512893] is NA. 
You could filter these out, e.g., ar[!is.na(position(ar)) & 
!is.na(position(ar))] or identify why these are read in in the first 
place using the 'param' argument as described on ?readAligned.

Martin

>
> If this is the case the problem is not in nucleR, maybe there are some
> rows in a strange format in the AlignedRead (could be due the multiple
> format changes) that may avoid the conversion to the RangedData. Maybe I
> can detect them and skip those cases, but I would need to see what's
> happening in that odd case.
>
> Let me know if there's something I can do.
>
> Regards,
>
> Oscar
>
>
> El 03/11/2011 13:58, Stefanie Ververs escribió:
>> Hi Oscar,
>>
>> thanks for your quick answer - I think I would have contacted you, if
>> there were no answers on the bioconductor-mailinglist.
>>
>> I just tried the workaround as you suggested, but I got the same error
>> again:
>> Fehler in solveUserSEW0(start = start, end = end, width = width) :
>> solving row 16512893: range cannot be determined from the supplied
>> arguments (too many NAs)
>> Calls: RangedData -> is -> IRanges -> solveUserSEW0 -> .Call
>>
>> I'll think about how to show you the data (it's hosted and processed
>> with Galaxy, so it might be possible to share it.)
>>
>> Regards,
>>
>> Steffi
>>
>> On 03.11.2011 13:16, Oscar Flores wrote:
>>> Hi Stefanie,
>>>
>>> I'm the developer of nucleR, so let's see if I can help you ;)
>>>
>>> After the processing, processReads converts the input data to a
>>> RangedData
>>> object for a easier manipulation later, so this error is occurs at
>>> the last
>>> step of the call, but data can be messed in previous steps. It's
>>> hard to tell what is happening without having a look to the input data,
>>> which I guess is huge...
>>>
>>> I would like to have a look to the raw data, but I know it is difficult
>>> to send it if it's not in a public repository. Maybe you can contact me
>>> directly about that (oflores at mmb.pcb.ub.es)...
>>>
>>> Meanwhile, if you want to try a workaround, you can directly convert the
>>> imported reads to RangedData format (which is the other format supported
>>> by processReads):
>>>
>>> (being "ar" your imported AlignedReads object)
>>>
>>> res = RangedData(IRanges(start=position(ar),width=width(ar)),
>>> strand=strand(ar),space=ar at chromosome)
>>>
>>> reads_pair = processReads(res, type="paired", fragmentLen=fragment_len)
>>>
>>> This should work, but will be nice to have a look to your data
>>> to fix a possible problem in the AlignedReads method.
>>>
>>> Regards,
>>>
>>> Oscar
>>>
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>>
>


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