XStringQuality-class {Biostrings} | R Documentation |
PhredQuality, SolexaQuality and IlluminaQuality objects
Description
Objects for storing string quality measures.
Usage
## 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
,
PairwiseAlignments-class,
DNAString-class,
BStringSet-class
Examples
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