# Working with modified nucleotide sequences

## Documentation for package ‘Modstrings’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

==-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
ModString | ModString objects
ModString-method | ModString objects
Modstrings | Modstrings: implementation of Biostrings to work with nucleotide sequences containing modified nucleotides.
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
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
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