MaskedXString-class {Biostrings} | R Documentation

## 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

[Package Biostrings version 2.56.0 Index]