[BioC] ShortReadQ constructor

Martin Morgan mtmorgan at fhcrc.org
Tue Oct 8 02:31:17 CEST 2013


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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