```
## Constructors:
PhredQuality(x)
SolexaQuality(x)
IlluminaQuality(x)
## alphabet and encoding
"alphabet"(x)
"encoding"(x)
```

x

Either a character vector, BString, BStringSet,
integer vector, or number vector of error probabilities.

`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