| MaskedXString-class {Biostrings} | R Documentation |
The MaskedBString, MaskedDNAString, MaskedRNAString and MaskedAAString classes are containers for storing masked sequences.
All those containers derive directly (and with no additional slots) from the MaskedXString virtual class.
In Biostrings, a pile of masks can be put on top of a sequence. A pile of masks is represented by a MaskCollection object and the sequence by an XString object. A MaskedXString object is the result of bundling them together in a single object.
Note that, no matter what masks are put on top of it, the original sequence is always stored unmodified in a MaskedXString object. This allows the user to activate/deactivate masks without having to worry about losing the information stored in the masked/unmasked regions. Also this allows efficient memory management since the original sequence never needs to be copied (modifying it would require to make a copy of it first - sequences cannot and should never be modified in place in Biostrings), even when the set of active/inactive masks changes.
In the code snippets below, x is a MaskedXString object.
For masks(x) and masks(x) <- y, it can also be
an XString object and y must be NULL or
a MaskCollection 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.
masks(x) <- y:
If x is an XString object and y is NULL,
then this doesn't do anything.
If x is an XString object and y is a
MaskCollection object, then
this turns x into a MaskedXString object by putting the
masks in y on top of it.
If x is a MaskedXString object and y is NULL,
then this is equivalent to x <- unmasked(x).
If x is a MaskedXString object and y is a
MaskCollection object, then
this replaces the masks currently on top of x by the masks
in y.
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).
In the code snippets below, x is a MaskedXString object.
as(x, "Views"):
Turns x into a Views object where the
views are the unmasked regions of the original sequence
("unmasked" means not masked by at least one active mask).
In the code snippets below, x is a MaskedXString object.
collapse(x):
Collapses the set of masks in x into a single mask made of
all active masks.
gaps(x):
Reverses all the masks i.e. each mask is replaced by a mask
where previously unmasked regions are now masked and
previously masked regions are now unmasked.
H. Pagès
## ---------------------------------------------------------------------
## A. MASKING BY POSITION
## ---------------------------------------------------------------------
mask0 <- Mask(mask.width=29, start=c(3, 10, 25), width=c(6, 8, 5))
x <- DNAString("ACACAACTAGATAGNACTNNGAGAGACGC")
length(x) # same as width(mask0)
nchar(x) # same as length(x)
masks(x) <- mask0
x
length(x) # has not changed
nchar(x) # has changed
gaps(x)
## Prepare a MaskCollection object of 3 masks ('mymasks') by running the
## examples in the man page for these objects:
example(MaskCollection, package="IRanges")
## Put it on 'x':
masks(x) <- mymasks
x
alphabetFrequency(x)
## Deactivate all masks:
active(masks(x)) <- FALSE
x
## Activate mask "C":
active(masks(x))["C"] <- TRUE
x
## Turn MaskedXString object into a Views object:
as(x, "Views")
## Drop the masks:
masks(x) <- NULL
x
alphabetFrequency(x)
## ---------------------------------------------------------------------
## B. MASKING BY CONTENT
## ---------------------------------------------------------------------
## See ?maskMotif for masking by content