Perform pairwise sequence alignments


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Documentation for package ‘pwalign’ version 1.2.0

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A B C D E I L M N P Q R S T U V W

-- A --

align-utils Utility functions related to sequence alignment
aligned AlignedXStringSet and QualityAlignedXStringSet objects
aligned-method AlignedXStringSet and QualityAlignedXStringSet objects
aligned-method PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
alignedPattern PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
alignedPattern-method PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
alignedSubject PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
alignedSubject-method PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
AlignedXStringSet AlignedXStringSet and QualityAlignedXStringSet objects
AlignedXStringSet-class AlignedXStringSet and QualityAlignedXStringSet objects
AlignedXStringSet0 AlignedXStringSet and QualityAlignedXStringSet objects
AlignedXStringSet0-class AlignedXStringSet and QualityAlignedXStringSet objects
as.character-method AlignedXStringSet and QualityAlignedXStringSet objects
as.character-method PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
as.matrix-method PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects

-- B --

BLOSUM100 Predefined scoring matrices
BLOSUM45 Predefined scoring matrices
BLOSUM50 Predefined scoring matrices
BLOSUM62 Predefined scoring matrices
BLOSUM80 Predefined scoring matrices

-- C --

class:AlignedXStringSet AlignedXStringSet and QualityAlignedXStringSet objects
class:AlignedXStringSet0 AlignedXStringSet and QualityAlignedXStringSet objects
class:InDel InDel objects
class:PairwiseAlignments PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
class:PairwiseAlignmentsSingleSubject PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
class:PairwiseAlignmentsSingleSubjectSummary PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
class:QualityAlignedXStringSet AlignedXStringSet and QualityAlignedXStringSet objects
compareStrings Utility functions related to sequence alignment
compareStrings-method Utility functions related to sequence alignment
consensusMatrix-method Utility functions related to sequence alignment
coverage-method Utility functions related to sequence alignment

-- D --

deletion InDel objects
deletion-method InDel objects
deletion-method PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects

-- E --

end-method AlignedXStringSet and QualityAlignedXStringSet objects
errorSubstitutionMatrices Utilities to generate substitution matrices

-- I --

InDel InDel objects
indel AlignedXStringSet and QualityAlignedXStringSet objects
InDel-class InDel objects
indel-method AlignedXStringSet and QualityAlignedXStringSet objects
indel-method PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
insertion InDel objects
insertion-method InDel objects
insertion-method PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects

-- L --

length-method PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects

-- M --

mismatch-method Utility functions related to sequence alignment
mismatchSummary Utility functions related to sequence alignment
mismatchSummary-method Utility functions related to sequence alignment
mismatchTable Utility functions related to sequence alignment
mismatchTable-method Utility functions related to sequence alignment

-- N --

nchar-method AlignedXStringSet and QualityAlignedXStringSet objects
nchar-method PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
nedit Utility functions related to sequence alignment
nedit-method Utility functions related to sequence alignment
nindel AlignedXStringSet and QualityAlignedXStringSet objects
nindel-method AlignedXStringSet and QualityAlignedXStringSet objects
nindel-method PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
nmatch-method Utility functions related to sequence alignment
nmismatch-method Utility functions related to sequence alignment
nucleotideSubstitutionMatrix Utilities to generate substitution matrices

-- P --

pairwiseAlignment Optimal Pairwise Alignment
pairwiseAlignment-method Optimal Pairwise Alignment
PairwiseAlignments PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
PairwiseAlignments-class PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
PairwiseAlignments-io Write a PairwiseAlignments object to a file
PairwiseAlignments-method PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
PairwiseAlignmentsSingleSubject PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
PairwiseAlignmentsSingleSubject-class PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
PairwiseAlignmentsSingleSubject-method PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
PairwiseAlignmentsSingleSubjectSummary PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
PairwiseAlignmentsSingleSubjectSummary-class PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
PAM120 Predefined scoring matrices
PAM250 Predefined scoring matrices
PAM30 Predefined scoring matrices
PAM40 Predefined scoring matrices
PAM70 Predefined scoring matrices
parallelVectorNames-method AlignedXStringSet and QualityAlignedXStringSet objects
parallel_slot_names-method AlignedXStringSet and QualityAlignedXStringSet objects
parallel_slot_names-method PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
pattern-method PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
phiX174Phage Versions of bacteriophage phiX174 complete genome and sample short reads
pid Percent Sequence Identity
pid-method Percent Sequence Identity
predefined_scoring_matrices Predefined scoring matrices

-- Q --

QualityAlignedXStringSet AlignedXStringSet and QualityAlignedXStringSet objects
QualityAlignedXStringSet-class AlignedXStringSet and QualityAlignedXStringSet objects
qualitySubstitutionMatrices Utilities to generate substitution matrices
quPhiX174 Versions of bacteriophage phiX174 complete genome and sample short reads

-- R --

ranges-method AlignedXStringSet and QualityAlignedXStringSet objects

-- S --

score-method PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
seqtype-method AlignedXStringSet and QualityAlignedXStringSet objects
seqtype-method PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
show-method AlignedXStringSet and QualityAlignedXStringSet objects
show-method PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
srPhiX174 Versions of bacteriophage phiX174 complete genome and sample short reads
start-method AlignedXStringSet and QualityAlignedXStringSet objects
stringDist String Distance/Alignment Score Matrix
stringDist-method String Distance/Alignment Score Matrix
subject-method PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
substitution_matrices Utilities to generate substitution matrices
summary-method PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects

-- T --

toString-method AlignedXStringSet and QualityAlignedXStringSet objects
toString-method PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
type PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects
type-method PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects

-- U --

unaligned AlignedXStringSet and QualityAlignedXStringSet objects
unaligned-method AlignedXStringSet and QualityAlignedXStringSet objects

-- V --

Views-method PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects

-- W --

width-method AlignedXStringSet and QualityAlignedXStringSet objects
writePairwiseAlignments Write a PairwiseAlignments object to a file
wtPhiX174 Versions of bacteriophage phiX174 complete genome and sample short reads