ShortRead-class {ShortRead} | R Documentation

## "ShortRead" class for short reads

### Description

This class provides a way to store and manipulate, in a coordinated fashion, uniform-length short reads and their identifiers.

### Objects from the Class

Objects from this class are created by `readFasta`, or by calls to the constructor `ShortRead`, as outlined below.

### Slots

`sread`:

  Object of class `"DNAStringSet"` containing IUPAC-standard, uniform-length DNA strings represent short sequence reads.

`id`:

  Object of class `"BStringSet"` containing identifiers, one for each short read.

### Extends

Class `".ShortReadBase"`, directly.

### Methods

Constructors include:

ShortRead

  `signature(sread = "DNAStringSet", id = "BStringSet")`: Create a `ShortRead` object from reads and their identifiers. The length of `id` must match that of `sread`.

ShortRead

  `signature(sread = "DNAStringSet", id = "missing")`: Create a `ShortRead` object from reads, creating empty identifiers.

ShortRead

  `signature(sread = "missing", id = "missing")`: Create an empty `ShortRead` object.

Methods include:

sread

  `signature(object = "AlignedRead")`: access the sread slot of `object`. `as(object, "DNAStringSet")` is similar, but adds `id(object)` as the `names()` of the DNAStringSet.

id

  `signature(object = "AlignedRead")`: access the id slot of `object`.

[

  `signature(x = "ShortRead", i = "ANY", j = "missing")`: This method creates a new `ShortRead` object containing only those reads indexed by `i`. Additional methods on ‘[,ShortRead’ do not provide additional functionality, but are present to limit inappropriate use.

append

  `signature(x = "ShortRead", values = "ShortRead")`: append the `sread` and `id` slots of `values` after the corresponding fields of `x`.

narrow

  `signature(x = "ShortRead", start = NA, end = NA, width = NA, use.names = TRUE)`: ‘narrow’ `sread` so that sequences are between `start` and `end` bases, according to `narrow` in the `IRanges` package.

length

  `signature(x = "ShortRead")`: returns a `integer(1)` vector describing the number of reads in this object.

width

  `signature(x = "ShortRead")`: returns an `integer()` vector of the widths of each read in this object.

srorder

  `signature(x = "ShortRead")`:

srrank

  `signature(x = "ShortRead")`:

srsort

  `signature(x = "ShortRead")`:

srduplicated

  `signature(x = "ShortRead")`: Order, rank, sort, and find duplicates in `ShortRead` objects based on `sread(x)`, analogous to the corresponding functions `order`, `rank`, `sort`, and `duplicated`, ordering nucleotides in the order `ACGT`.

srdistance

  `signature(pattern="ShortRead", subject="ANY")`: Find the edit distance between each read in `pattern` and the (short) sequences in `subject`. See `srdistance` for allowable values for `subject`, and for additional details.

trimLRPatterns

  `signature(Lpattern = "", Rpattern = "", subject = "ShortRead", max.Lmismatch = 0, max.Rmismatch = 0, with.Lindels = FALSE, with.Rindels = FALSE, Lfixed = TRUE, Rfixed = TRUE, ranges = FALSE)`:

  Remove left and / or right flanking patterns from `sread(subject)`, as described in `trimLRPatterns`. Classes derived from `ShortRead` (e.g., `ShortReadQ`, `AlignedRead`) have corresponding base quality scores trimmed, too. The class of the return object is the same as the class of `subject`, except when `ranges=TRUE` when the return value is the ranges to use to trim 'subject'.

alphabetByCycle

  `signature(stringSet = "ShortRead")`: Apply `alphabetByCycle` to the `sread` component of `stringSet`, returning a matrix as described in `alphabetByCycle`.

tables

  `signature(x= "ShortRead", n = 50)`: Apply `tables` to the `sread` component of `x`, returning a list summarizing frequency of reads in `x`.

clean

  `signature(object="ShortRead")`: Remove all reads containing non-nucleotide (`"N", "-"`) symbols.

show

  `signature(object = "ShortRead")`: provides a brief summary of the object, including its class, length and width.

detail

  `signature(x = "ShortRead")`: provides a more extensive summary of this object, displaying the first and last entries of `sread` and `id`.

writeFasta

  `signature(object, file, ...)`: write `object` to `file` in fasta format. See `writeXStringSet` for `...` argument values.

### Author(s)

Martin Morgan

### See Also

`ShortReadQ`

### Examples

    showClass("ShortRead")
    showMethods(class="ShortRead", where=getNamespace("ShortRead"))

[Package ShortRead version 1.52.0 Index]