PhredQuality, SolexaQuality and IlluminaQuality objects
Objects for storing string quality measures.
## Constructors: PhredQuality(x) SolexaQuality(x) IlluminaQuality(x) ## alphabet and encoding ## S4 method for signature 'XStringQuality' alphabet(x) ## S4 method for signature 'XStringQuality' encoding(x)
x |
Either a character vector, BString, BStringSet, integer vector, or number vector of error probabilities. |
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)
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. Use as.integer and as.numeric to
coerce objects to their integer and probability representations.
P. Aboyoun
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 scoresPlease choose more modern alternatives, such as Google Chrome or Mozilla Firefox.