| QualityScaledXStringSet-class {Biostrings} | R Documentation |
The QualityScaledBStringSet class is a container for storing a
BStringSet object with an XStringQuality object.
Similarly, the QualityScaledDNAStringSet (or QualityScaledRNAStringSet, or
QualityScaledAAStringSet) class is a container for storing a DNAStringSet
(or RNAStringSet, or AAStringSet) objects with
an XStringQuality object.
## Constructors: QualityScaledBStringSet(x, quality) QualityScaledDNAStringSet(x, quality) QualityScaledRNAStringSet(x, quality) QualityScaledAAStringSet(x, quality)
x |
Either a character vector, or an XString, XStringSet or XStringViews object. |
quality |
An XStringQuality object. |
The QualityScaledBStringSet, QualityScaledDNAStringSet,
QualityScaledRNAStringSet and QualityScaledAAStringSet
functions are constructors that can be used to "naturally" turn
x into an QualityScaledXStringSet object of the desired base type.
The QualityScaledXStringSet class derives from the XStringSet
class hence all the accessor methods defined for an XStringSet
object can also be used on an QualityScaledXStringSet object. Common
methods include (in the code snippets below, x is an
QualityScaledXStringSet object):
length(x):
The number of sequences in x.
width(x):
A vector of non-negative integers containing the number
of letters for each element in x.
nchar(x):
The same as width(x).
names(x):
NULL or a character vector of the same length as x containing
a short user-provided description or comment for each element in x.
quality(x):
The quality of the strings.
In the code snippets below,
x and values are XStringSet objects,
and i should be an index specifying the elements to extract.
x[i]:
Return a new QualityScaledXStringSet object made of the selected elements.
P. Aboyoun
BStringSet-class, DNAStringSet-class, RNAStringSet-class, AAStringSet-class, XStringQuality-class
x1 <- DNAStringSet(c("TTGA", "CTCN"))
q1 <- PhredQuality(c("*+,-", "6789"))
qx1 <- QualityScaledDNAStringSet(x1, q1)
qx1