clean {ShortRead} | R Documentation

## Remove sequences with ambiguous nucleotides from short read classes

### Description

Short reads may contain ambiguous base calls (i.e., IUPAC symbols different from A, T, G, C). This generic removes all sequences containing 1 or more ambiguous bases.

### Usage

    clean(object, ...)

### Arguments

`object` | An object for which `clean` methods exist; see below to discover these methods.
`...` | Additional arguments, perhaps used by methods.

### Details

The following method is defined, in addition to methods described in class-specific documentation:

clean

  `signature(x = "DNAStringSet")`: Remove all sequences containing non-base (A, C, G, T) IUPAC symbols.

### Value

An instance of `class(object)`, containing only sequences with non-redundant nucleotides.

### Author(s)

Martin Morgan <mtmorgan@fhcrc.org>

### Examples

    showMethods('clean')

[Package ShortRead version 1.42.0 Index]