MaskedXString-class {Biostrings} | R Documentation

## MaskedXString objects

### Description

The MaskedXString class is a container for storing a masked sequence.

### Details

[TODO]

### Accesor methods

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.

### "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

TODO

### Other methods

TODO

### Author(s)

H. Pages

### See Also

`maskMotif`, `alphabetFrequency`, `reverse`, XString-class, MaskCollection-class, XStringViews-class, IRanges-utils

### Examples

      ## 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

[Package Biostrings version 2.8.18 Index]