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