clean: Remove sequences with ambiguous nucleotides from short read...
In Bioconductor/ShortRead: FASTQ input and manipulation
clean 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')
Bioconductor/ShortRead documentation built on May 5, 2024, 4:14 a.m.
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| clean | 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 |
... |
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')
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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