Remove sequences with ambiguous nucleotides from short read classes
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.
clean(object, ...)
object |
An object for which |
... |
Additional arguments, perhaps used by methods. |
The following method is defined, in addition to methods described in class-specific documentation:
signature(x = "DNAStringSet"):
Remove all sequences containing non-base (A, C, G, T) IUPAC
symbols.
An instance of class(object), containing only sequences with
non-redundant nucleotides.
Martin Morgan <mtmorgan@fhcrc.org>
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