[BioC] ShortReadQ constructor

Ivan Gregoretti ivangreg at gmail.com
Tue Oct 8 02:44:41 CEST 2013


The renew() looks really handy. The direct use of the constructor is
something that I tried but failed to me. I probably had one of those
invisible typos.

Thank you.

Ivan


Ivan Gregoretti, PhD
Bioinformatics
Cell Signaling Technology, Inc
3 Trask Lane
Danvers, MA 01923. USA.
Phone +1-978-867-2429


On Mon, Oct 7, 2013 at 8:31 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> On 10/07/2013 05:06 PM, Ivan Gregoretti wrote:
>>
>> Hello Martin,
>>
>> Great. So,
>>
>> srq1 <- ShortReadQ(DNAStringSet(c("ACGT", "GGGGACT")),
>> FastqQuality(c("HHHH", "HHHHHHH")), BStringSet(c("read1", "read2")))
>>
>> gets me what I wanted. Now I have a part two to my question:
>>
>> How do I modify srq1's id?
>>
>> For instance, id(srq1) produces
>>
>>> id(srq1)
>>
>>    A BStringSet instance of length 2
>>      width seq
>> [1]     5 read1
>> [2]     5 read2
>>
>> but I want to modify srq1's id so that it looks like this
>>
>>> BStringSet(paste(id(srq1), 'tested'))
>>
>>    A BStringSet instance of length 2
>>      width seq
>> [1]    12 read1 tested
>> [2]    12 read2 tested
>>
>> Please note that I intend not to construct a new instance by passing
>> FastqQuality(c("HHHH", "HHHHHHH")) and DNAStringSet(c("ACGT",
>> "GGGGACT")). I intend to copy srq1 to srq2 and then modify srq2.
>>
>
> ShortRead explored the notion of a 'renw'able instance, see ?renew and
>
>   srq2 = renew(srq1, id=BStringSet(paste(id(srq1), "tested")))
>
> this
>
>   ShortReadQ(sread(srq1), quality(srq1), BStringSet(paste(id(srq1),
> "tested")))
>
> also works
>
> Martin
>
>
>> Alternatively, may I construct a new instance by passing
>> BStringSet(paste(id(srq1), 'tested')), sread(srq1) and quality(srq1)?
>> I tried by the constructor complained vociferously when I passed
>> quality=quality(srq1).
>>
>> Thank you,
>>
>> Ivan
>>
>>
>>
>>
>> Ivan Gregoretti, PhD
>> Bioinformatics
>>
>>
>>
>>
>> On Mon, Oct 7, 2013 at 3:44 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
>>>
>>> On 10/07/2013 12:28 PM, Ivan Gregoretti wrote:
>>>>
>>>>
>>>> Hello,
>>>>
>>>> Could somebody show an example of constructing a ShortReadQ object
>>>> instance? I can't find an example in the documentation.
>>>>
>>>>
>>>> For example, lets say that I have two records with the following ids,
>>>> sequences, and Phred qualities
>>>>
>>>> c("read1", "read2")
>>>> c("ACGT", "GGGGACT")
>>>> c("HHHH", "HHHHHHH")
>>>>
>>>> How would you now construct the ShortReadQ instance?
>>>
>>>
>>>
>>> Hi Ivan
>>>
>>> ShortReadQ(DNAStringSet(c("ACGT", "GGGGACT")),
>>>      FastqQuality(c("HHHH", "HHHHHHH")),
>>>      BStringSet(c("read1", "read2")))
>>>
>>> Martin
>>>
>>>>
>>>> Thank you,
>>>>
>>>> Ivan
>>>>
>>>>
>>>>
>>>>
>>>> Ivan Gregoretti, PhD
>>>> Bioinformatics
>>>>
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>>>
>>>
>>> --
>>> Computational Biology / Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N.
>>> PO Box 19024 Seattle, WA 98109
>>>
>>> Location: Arnold Building M1 B861
>>> Phone: (206) 667-2793
>
>
>
> --
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793



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