![]() ReverseComplement(x) is equivalent to reverse(complement(x))Īn object of the same class and length as the original object. ![]() W W, H D, N N) and the gap ( "-") and hard masking Replaced by their complement (M K, R Y, S S, V B, Letters belonging to the IUPAC Extended Genetic Alphabet are also A, C, G, T in a DNAString object are replacedīy T, G, C, A respectively and A, C, G, U in a RNAString object MaskedDNAString or MaskedRNAString objectĪdditional arguments to be passed to or from methods.Ĭomplement(x) returns an object where each base in x XStringViews (with DNAString or RNAString subject), stringDist: String Distance/Alignment Score MatrixĬomplement ( x.reverseComplement: Sequence reversing and complementing.replaceLetterAt: Replacing letters in a sequence (or set of sequences) at some.replaceAt: Extract/replace arbitrary substrings from/in a string or set.QualityScaledXStringSet-class: QualityScaledBStringSet, QualityScaledDNAStringSet.pmatchPattern: Longest Common Prefix/Suffix/Substring searching functions.phiX174Phage: Versions of bacteriophage phiX174 complete genome and sample.PairwiseAlignments-io: Write a PairwiseAlignments object to a file.PairwiseAlignments-class: PairwiseAlignments, PairwiseAlignmentsSingleSubject, and.pairwiseAlignment: Optimal Pairwise Alignment.nucleotideFrequency: Calculate the frequency of oligonucleotides in a DNA or RNA.needwunsQS: (Deprecated) Needleman-Wunsch Global Alignment.MultipleAlignment-class: MultipleAlignment objects.match-utils: Utility functions operating on the matches returned by a.matchPWM: PWM creating, matching, and related utilities.matchprobes: A function to match a query sequence to the sequences of a.matchProbePair: Find "theoretical amplicons" mapped to a probe pair.matchPDict-inexact: Inexact matching with matchPDict()/countPDict()/whichPDict().matchPDict-exact: Matching a dictionary of patterns against a reference.matchPattern: String searching functions.matchLRPatterns: Find paired matches in a sequence.maskMotif: Masking by content (or by position).MaskedXString-class: MaskedXString objects.lowlevel-matching: Low-level matching functions.longestConsecutive: Obtain the length of the longest substring containing only.letterFrequency: Calculate the frequency of letters in a biological sequence.IUPAC_CODE_MAP: The IUPAC Extended Genetic Alphabet.injectHardMask: Injecting a hard mask in a sequence. ![]() ![]()
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