PhredQuality, SolexaQuality and IlluminaQuality objects
Description
Objects for storing string quality measures.
Usage
1 2 3 4 5 6 7 8 9 10  ## Constructors:
PhredQuality(x)
SolexaQuality(x)
IlluminaQuality(x)
## alphabet and encoding
## S4 method for signature 'XStringQuality'
alphabet(x)
## S4 method for signature 'XStringQuality'
encoding(x)

Arguments
x 
Either a character vector, BString, BStringSet, integer vector, or number vector of error probabilities. 
Details
PhredQuality
objects store characters that are interpreted as
[0  99] quality measures by subtracting 33 from their ASCII decimal
representation (e.g. ! = 0, " = 1, \# = 2, ...). Quality measures q
encode probabilities as 10 * log10(p)
.
SolexaQuality
objects store characters that are interpreted as
[5  99] quality measures by subtracting 64 from their ASCII decimal
representation (e.g. ; = 5, < = 4, = = 3, ...). Quality measures q
encode probabilities as 10 * (log10(p)  log10(1  p))
.
IlluminaQuality
objects store characters that are interpreted
as [0  99] quality measures by subtracting 64 from their ASCII
decimal representation (e.g. @ = 0, A = 1, B = 2, ...). Quality
measures q encode probabilities as 10 * log10(p)
Alphabet and encoding
In the code snippets below, x
is an XStringQuality object.

alphabet(x)
: Valid letters in this quality score; not all letters are encountered in actual sequencing runs. 
encoding(x)
: Map between letters and their corresponding integer encoding. Useas.integer
andas.numeric
to coerce objects to their integer and probability representations.
Author(s)
P. Aboyoun
See Also
pairwiseAlignment
,
PairwiseAlignmentsclass,
DNAStringclass,
BStringSetclass
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19  PhredQuality(0:40)
SolexaQuality(0:40)
IlluminaQuality(0:40)
pq < PhredQuality(c("*+,./", "0123456789:;"))
qs < as(pq, "IntegerList") # quality scores
qs
as(qs, "PhredQuality")
p < as(pq, "NumericList") # probabilities
as(p, "PhredQuality")
PhredQuality(seq(1e4,0.5,length=10))
SolexaQuality(seq(1e4,0.5,length=10))
IlluminaQuality(seq(1e4,0.5,length=10))
x < SolexaQuality(BStringSet(c(a="@ABC", b="abcd")))
as(x, "IntegerList") # quality scores
as(x, "NumericList") # probabilities
as.matrix(x) # quality scores

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