## Constructors:
PhredQuality(x)
SolexaQuality(x)
IlluminaQuality(x)
## alphabet and encoding
"alphabet"(x)
"encoding"(x)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. Use as.integer and as.numeric to
coerce objects to their integer and probability representations.
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)
pairwiseAlignment,
PairwiseAlignments-class,
DNAString-class,
BStringSet-class
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(1e-4,0.5,length=10))
SolexaQuality(seq(1e-4,0.5,length=10))
IlluminaQuality(seq(1e-4,0.5,length=10))
x <- SolexaQuality(BStringSet(c(a="@ABC", b="abcd")))
as(x, "IntegerList") # quality scores
as(x, "NumericList") # probabilities
as.matrix(x) # quality scores