MaskedXString-class: MaskedXString objects

In Bioconductor/Biostrings: Efficient manipulation of biological strings

MaskedXString objects

Description

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.

Details

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.

Accessor methods

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.

"maskedwidth" and related methods

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).

Coercion

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).

Other methods

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.

Author(s)

H. Pagès

See Also

• maskMotif

• injectHardMask

• alphabetFrequency

• reverseComplement

• XString-class

• MaskCollection-class

• Views-class

Examples

## ---------------------------------------------------------------------
## 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

Bioconductor/Biostrings documentation built on Dec. 16, 2024, 8:46 a.m.