[BioC] how does ShortRead function identify score system

[wang peter]

dear ALL:
       i have many RNA-seq data.
some use Phred+33 system to score the quality
some use Phred+63

i found no parameter to tell the functions which one should be.
but it still works
can you tell me which function can identify them.

such is the coding:
reads <- readFastq(fastqfile);

qual <- FastqQuality(quality(quality(reads)));
#qual <- PhredQuality(quality(quality(reads)));#

readM <- as(qual, "matrix");#注意R's maximum vector length is 2^31 - 1
pdf(file="boxplot.pdf"); # Save box plot as boxplot.pdf in current folder
boxplot(as.data.frame((readM)), outline = FALSE, main="Per Cycle Read
Quality", xlab="Cycle", ylab="Phred Quality");
# build per cycle boxplot

-- 
shan gao
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Boyce Thompson Institute
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