| MaskedXString-class {Biostrings} | R Documentation |
The MaskedXString class is a container for storing a masked sequence.
[TODO]
In the code snippets below, x is a MaskedXString object.
unmasked(x):
Turns x into an XString object by dropping the masks.
masks(x):
Turns x into a MaskCollection object by dropping the sequence.
alphabet(x):
Equivalent to alphabet(unmasked(x)).
See ?alphabet for more information.
length(x):
Equivalent to length(unmasked(x)).
See ?`length,XString-method` for more information.
In the code snippets below, x is a MaskedXString object.
maskedwidth(x):
Get the number of masked letters in x. A letter is considered
masked iff it's masked by at least one active mask.
maskedratio(x):
Equivalent to maskedwidth(x) / length(x).
nchar(x):
Equivalent to length(x) - maskedwidth(x).
TODO
TODO
H. Pages
maskMotif,
alphabetFrequency,
reverse,
XString-class,
MaskCollection-class,
XStringViews-class,
IRanges-utils
## Masking by position
mask0 <- Mask(mask.width=29, start=c(3, 10, 25), width=c(6, 8, 5))
x <- DNAString("ACACAACTAGATAGNACTNNGAGAGACGC")
masks(x) <- mask0
x
gaps(x)
## See ?maskMotif for masking by content