[BioC] Typo in ?FastqQuality help page?

[Peng Yu]

On Sat, May 22, 2010 at 5:44 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> On 05/22/2010 03:38 PM, Peng Yu wrote:
>> Hi Martin,
>>
>> '?FastqQuality' leads me to page with the first line 'QualityScore
>>         package:ShortRead             R Documentation'
>>
>> Then I see,
>>
>>      Use these functions to construct quality indicators for reads or
>>      alignments. See 'QualityScore' for details of object content and
>>      methods available for manipulating them.
>> ...
>>      Constructors return objects of the corresponding class derived
>>      from 'QualityScore'.
>>
>> ...
>>      'QualityScore', 'readFastq', 'readAligned'
>>
>>
>> However, when I query the helppage of QualityScore, I got nothing.
>>
>>> ?QualityScore
>> No documentation for 'QualityScore' in specified packages and libraries:
>> you could try '??QualityScore'
>
> ?"QualityScore-class"

I don't see where the explanation of the difference between
FastqQuality and SFastqQuality is. Is the first one for Sanger the
second one for Illumina according to the following webpage?

http://en.wikipedia.org/wiki/FASTQ_format

There are totally 4 different Phred score scheme. Would you please let
which correspond to which class in ShortRead package?

S - Sanger        Phred+33,  raw reads typically (0, 40)
 X - Solexa        Solexa+64, raw reads typically (-5, 40)
 I - Illumina 1.3+ Phred+64,  raw reads typically (0, 40)
 J - Illumina 1.5+ Phred+64,  raw reads typically (3, 40) with
0=unused, 1=unused, 2=Read Segment Quality Control Indicator (bold)

-- 
Regards,
Peng