Working with modified nucleotide sequences

Documentation for package ‘Modstrings’ version 1.20.0

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==-method	ModString objects
==-method	ModStringSet objects
==-method	The ModStringViews class extending the XStringViews class
alphabet	Base information for sequence characters of nucleotide strings containing modifications
alphabet-method	Base information for sequence characters of nucleotide strings containing modifications
alphabetFrequency	Calculate the frequency of letters in nucleotide sequence with modifications, or the consensus matrix of a set of sequences
alphabetFrequency-method	Calculate the frequency of letters in nucleotide sequence with modifications, or the consensus matrix of a set of sequences
as.character-method	ModString objects
as.character-method	ModStringSet objects
as.vector-method	ModString objects
combineIntoModstrings	Separating and combining a modification information into/from a 'XString' and a 'GRanges' object
combineIntoModstrings-method	Separating and combining a modification information into/from a 'XString' and a 'GRanges' object
combineModifications	Separating and combining a modification information into/from a 'XString' and a 'GRanges' object
combineModifications-method	Separating and combining a modification information into/from a 'XString' and a 'GRanges' object
consensusMatrix-method	Calculate the frequency of letters in nucleotide sequence with modifications, or the consensus matrix of a set of sequences
consensusString	Calculate the frequency of letters in nucleotide sequence with modifications, or the consensus matrix of a set of sequences
consensusString-method	Calculate the frequency of letters in nucleotide sequence with modifications, or the consensus matrix of a set of sequences
fullName	Base information for sequence characters of nucleotide strings containing modifications
fullName-method	Base information for sequence characters of nucleotide strings containing modifications
hasOnlyBaseLetters	Calculate the frequency of letters in nucleotide sequence with modifications, or the consensus matrix of a set of sequences
hasOnlyBaseLetters-method	Calculate the frequency of letters in nucleotide sequence with modifications, or the consensus matrix of a set of sequences
incompatibleModifications	Separating and combining a modification information into/from a 'XString' and a 'GRanges' object
incompatibleModifications-method	Separating and combining a modification information into/from a 'XString' and a 'GRanges' object
letterFrequency	Calculate the frequency of letters in nucleotide sequence with modifications, or the consensus matrix of a set of sequences
letterFrequency-method	Calculate the frequency of letters in nucleotide sequence with modifications, or the consensus matrix of a set of sequences
letterFrequencyInSlidingView	Calculate the frequency of letters in nucleotide sequence with modifications, or the consensus matrix of a set of sequences
MaskedModString	MaskedModString objects
ModDNAString	ModDNAString class
ModDNAString-class	ModString objects
ModDNAStringSet	ModStringSet objects
ModDNAStringSet-class	ModStringSet objects
ModDNAStringSetList	ModStringSetList
ModDNAStringSetList-class	ModStringSetList
modifyNucleotides	Modifying nucleotides in a nucleotide sequence (or set of sequences) at specified locations
modifyNucleotides-method	Modifying nucleotides in a nucleotide sequence (or set of sequences) at specified locations
ModRNAString	ModDNAString class
ModRNAString-class	ModString objects
ModRNAStringSet	ModStringSet objects
ModRNAStringSet-class	ModStringSet objects
ModRNAStringSetList	ModStringSetList
ModRNAStringSetList-class	ModStringSetList
modsDNA	Modstrings internals
modsRNA	Modstrings internals
ModString	ModString objects
ModString-method	ModString objects
Modstrings	Modstrings: implementation of Biostrings to work with nucleotide sequences containing modified nucleotides.
Modstrings-internals	Modstrings internals
ModStringSet	ModStringSet objects
ModStringSet-io	Read/write an ModStringSet object from/to a file
ModStringSet-method	ModStringSet objects
ModStringSet-method	The ModStringViews class extending the XStringViews class
ModStringSetList	ModStringSetList
ModStringViews	The ModStringViews class extending the XStringViews class
MOD_RNA_DICT_MODOMICS	Modstrings internals
MOD_RNA_DICT_TRNADB	Modstrings internals
nomenclature	Base information for sequence characters of nucleotide strings containing modifications
nomenclature-method	Base information for sequence characters of nucleotide strings containing modifications
QualityScaledModDNAStringSet	QualityScaledModDNAStringSet and QualityScaledModRNAStringSet objects
QualityScaledModDNAStringSet-class	QualityScaledModDNAStringSet and QualityScaledModRNAStringSet objects
QualityScaledModRNAStringSet	QualityScaledModDNAStringSet and QualityScaledModRNAStringSet objects
QualityScaledModRNAStringSet-class	QualityScaledModDNAStringSet and QualityScaledModRNAStringSet objects
QualityScaledModStringSet	QualityScaledModDNAStringSet and QualityScaledModRNAStringSet objects
readModDNAStringSet	Read/write an ModStringSet object from/to a file
readModRNAStringSet	Read/write an ModStringSet object from/to a file
readQualityScaledModDNAStringSet	QualityScaledModDNAStringSet and QualityScaledModRNAStringSet objects
readQualityScaledModRNAStringSet	QualityScaledModDNAStringSet and QualityScaledModRNAStringSet objects
removeIncompatibleModifications	Separating and combining a modification information into/from a 'XString' and a 'GRanges' object
removeIncompatibleModifications-method	Separating and combining a modification information into/from a 'XString' and a 'GRanges' object
replaceLetterAt	Replacing letters in a nucleotide sequence (or set of nucleotide sequences) at some specified locations containing nucleotide modifications
replaceLetterAt-method	Replacing letters in a nucleotide sequence (or set of nucleotide sequences) at some specified locations containing nucleotide modifications
sanitizeFromModomics	Sanitize input strings for use with ModString classes
sanitizeFromtRNAdb	Sanitize input strings for use with ModString classes
sanitizeInput	Sanitize input strings for use with ModString classes
separate	Separating and combining a modification information into/from a 'XString' and a 'GRanges' object
separate-method	Separating and combining a modification information into/from a 'XString' and a 'GRanges' object
seqtype-method	MaskedModString objects
seqtype-method	Modstrings internals
seqtype<--method	Modstrings internals
shortName	Base information for sequence characters of nucleotide strings containing modifications
shortName-method	Base information for sequence characters of nucleotide strings containing modifications
show-method	ModStringSet objects
show-method	The ModStringViews class extending the XStringViews class
show-method	QualityScaledModDNAStringSet and QualityScaledModRNAStringSet objects
Views-method	The ModStringViews class extending the XStringViews class
writeModStringSet	Read/write an ModStringSet object from/to a file
writeQualityScaledModStringSet	QualityScaledModDNAStringSet and QualityScaledModRNAStringSet objects
XString-method	Modstrings internals
XStringSet-method	Modstrings internals