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