# Efficient Manipulation of Modified Oligonucleotide Sequences

## Documentation for package ‘XNAString’ version 1.2.2

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

## Help Pages

A B C D E H I L M N O P R S T U X misc

## -- A --

alphabetFrequency | XNAAlphabetFrequency returns letters frequency for a given object in base, sugar or backbone slot

## -- B --

backbone | Backbone setter/getter method
backbone-method | Backbone setter/getter method
backbone<- | Backbone setter/getter method
backbone<--method | Backbone setter/getter method
base | Base setter/getter method
base-method | Base setter/getter method
base<- | Base setter/getter method
base<--method | Base setter/getter method

## -- C --

changeBase | Translate base slot based on complementary bases dictionary. Base sequence in transformed using compl_target column.
charOrDNA-class | setClassUnion definitions
complementary_bases | Default XNAString complementarity dictionary
compl_dictionary | Compl_dictionary setter/getter method
compl_dictionary-method | Compl_dictionary setter/getter method
compl_dictionary<- | Compl_dictionary setter/getter method
compl_dictionary<--method | Compl_dictionary setter/getter method
concatDict | Concatenate HELM-symbol custom dictionary with built-in HELM-symbol dictionary (xna_dictionary)
conjugate3 | Conjugate3 setter/getter method
conjugate3-method | Conjugate3 setter/getter method
conjugate3<- | Conjugate3 setter/getter method
conjugate3<--method | Conjugate3 setter/getter method
conjugate5 | Conjugate5 setter/getter method
conjugate5-method | Conjugate5 setter/getter method
conjugate5<- | Conjugate5 setter/getter method
conjugate5<--method | Conjugate5 setter/getter method

## -- D --

default_backbone | Default_backbone setter/getter method
default_backbone-method | Default_backbone setter/getter method
default_backbone<- | Default_backbone setter/getter method
default_backbone<--method | Default_backbone setter/getter method
default_sugar | Default_sugar setter/getter method
default_sugar-method | Default_sugar setter/getter method
default_sugar<- | Default_sugar setter/getter method
default_sugar<--method | Default_sugar setter/getter method
dictionary | Dictionary setter/getter method
dictionary-method | Dictionary setter/getter method
dictionary<- | Dictionary setter/getter method
dictionary<--method | Dictionary setter/getter method
dinucleotideFrequency | XNADinucleotideFrequencyFun returns double letters frequency for a given object in base, sugar or backbone slot
dt2Set | Function which creates XNAstringSet object from table with base, sugar and backbone columns.
duplex_structure | Duplex_structure setter/getter method
duplex_structure-method | Duplex_structure setter/getter method
duplex_structure<- | Duplex_structure setter/getter method
duplex_structure<--method | Duplex_structure setter/getter method

## -- E --

extractionMethods | Create class which consists of XNAString objects given as a list

## -- H --

helm2String | Translate RNA from HELM notation to multi-string notation

## -- I --

initialize | Development of XNAString class aims at enabling efficient manipulation of modified oligonucleotide sequences. The class consists of the following slots: name, base, sugar, backbone, target, conjugate5, conjugate3, secondary_structure, duplex_structure, dictionary (HELM-string dictionary), compl_dictionary.
initialize-method | Development of XNAString class aims at enabling efficient manipulation of modified oligonucleotide sequences. The class consists of the following slots: name, base, sugar, backbone, target, conjugate5, conjugate3, secondary_structure, duplex_structure, dictionary (HELM-string dictionary), compl_dictionary.
instanceOf | Check on an object type

## -- L --

listOflists2Dt | Save list of lists as data.table

## -- M --

mimir2XnaDict | Reformat mimir table to XNA dictionary standards

## -- N --

name | Name setter/getter method
name-method | Name setter/getter method
name<- | Name setter/getter method
name<--method | Name setter/getter method

## -- O --

objects | Objects getter method for XNAStringSet class
objects-method | Objects getter method for XNAStringSet class

## -- P --

parseRnaHelmComponent | Parse monomers from HELM to multi-string notation
predictDuplexStructure | Compute Minimum Free Energy (MFE), and a corresponding secondary structure for two dimerized RNA sequences.
predictDuplexStructure-method | Compute Minimum Free Energy (MFE), and a corresponding secondary structure for two dimerized RNA sequences.
predictDuplexStructureFun | Compute Minimum Free Energy (MFE), and a corresponding secondary structure for two dimerized RNA sequences.
predictMfeStructure | Prediction of MFE structure with ViennaRNA package
predictMfeStructure-method | Prediction of MFE structure with ViennaRNA package
predictMfeStructureFun | Prediction of MFE structure with ViennaRNA package

## -- R --

replaceBase | Fucntion for replacing bases in XNAString object
reverseComplementFun | Reverse complement sequence based on dictionary

## -- S --

secondary_structure | Secondary_structure setter/getter method
secondary_structure-method | Secondary_structure setter/getter method
secondary_structure<- | Secondary_structure setter/getter method
secondary_structure<--method | Secondary_structure setter/getter method
seqAlphabetFrequency | Create set of functions and methods to calculate alphabet frequency in base, sugar and backbone slots
seqDinucleotideFrequency | Create set of functions and methods to calculate dinucleotide frequency in base, sugar and backbone slots
seqtype | Development of XNAString class aims at enabling efficient manipulation of modified oligonucleotide sequences. The class consists of the following slots: name, base, sugar, backbone, target, conjugate5, conjugate3, secondary_structure, duplex_structure, dictionary (HELM-string dictionary), compl_dictionary.
seqtype-method | Development of XNAString class aims at enabling efficient manipulation of modified oligonucleotide sequences. The class consists of the following slots: name, base, sugar, backbone, target, conjugate5, conjugate3, secondary_structure, duplex_structure, dictionary (HELM-string dictionary), compl_dictionary.
seqVectorAlphabetFrequency | seqVectorAlphabetFrequency function calculates frequency for strings vector
seqVectorDinucleotideFrequency | seqVectorDinucleotideFrequency function calculates frequency for strings vector
set2Dt | set2Dt function - changes XNAStringSet object to data.table
set2List | Define method to save XNAStringSet object as a list of XNAString objects
set2List-method | Define method to save XNAStringSet object as a list of XNAString objects
show-method | Development of XNAString class aims at enabling efficient manipulation of modified oligonucleotide sequences. The class consists of the following slots: name, base, sugar, backbone, target, conjugate5, conjugate3, secondary_structure, duplex_structure, dictionary (HELM-string dictionary), compl_dictionary.
show-method | Create class which consists of XNAString objects given as a list
showMethod | Development of XNAString class aims at enabling efficient manipulation of modified oligonucleotide sequences. The class consists of the following slots: name, base, sugar, backbone, target, conjugate5, conjugate3, secondary_structure, duplex_structure, dictionary (HELM-string dictionary), compl_dictionary.
siRNA_HELM | siRNA_HELM function takes XNAString object and returns pairing information for base slot. Works only for double stranded molecules.
sugar | Sugar setter/getter method
sugar-method | Sugar setter/getter method
sugar<- | Sugar setter/getter method
sugar<--method | Sugar setter/getter method

## -- T --

target | Target setter/getter method
target-method | Target setter/getter method
target<- | Target setter/getter method
target<--method | Target setter/getter method
typedListCheck | Check if all objects are of XNAString class and dictionaries are the same

## -- U --

uniqueChars | Utility functions useful when programming and developing XNAString class

## -- X --

XNAAlphabetFrequency | XNAAlphabetFrequency returns letters frequency for a given object in base, sugar or backbone slot
XNAAlphabetFrequency-method | XNAAlphabetFrequency returns letters frequency for a given object in base, sugar or backbone slot
XNAAlphabetFrequencyFun | XNAAlphabetFrequency returns letters frequency for a given object in base, sugar or backbone slot
XNADinucleotideFrequency | XNADinucleotideFrequencyFun returns double letters frequency for a given object in base, sugar or backbone slot
XNADinucleotideFrequency-method | XNADinucleotideFrequencyFun returns double letters frequency for a given object in base, sugar or backbone slot
XNADinucleotideFrequencyFun | XNADinucleotideFrequencyFun returns double letters frequency for a given object in base, sugar or backbone slot
XNAMatchPattern | Finds pattern in reference sequence
XNAMatchPattern-method | Finds pattern in reference sequence
XNAMatchPDict | Find set of patterns in reference sequence
XNAMatchPDict-method | Find set of patterns in reference sequence
xnaObj2Dt | xnaObj2Dt function - changes XNAString object to data.table
XNAPairwiseAlignment | Pairwise alignment methods for XNAString object
XNAPairwiseAlignment-method | Pairwise alignment methods for XNAString object
XNAReverseComplement | Reverse complement sequence based on dictionary
XNAReverseComplement-method | Reverse complement sequence based on dictionary
XNAString | Development of XNAString class aims at enabling efficient manipulation of modified oligonucleotide sequences. The class consists of the following slots: name, base, sugar, backbone, target, conjugate5, conjugate3, secondary_structure, duplex_structure, dictionary (HELM-string dictionary), compl_dictionary.
XNAString-class | Development of XNAString class aims at enabling efficient manipulation of modified oligonucleotide sequences. The class consists of the following slots: name, base, sugar, backbone, target, conjugate5, conjugate3, secondary_structure, duplex_structure, dictionary (HELM-string dictionary), compl_dictionary.
XNAString2XNAStringSet | XNAString2XNAStringSet function - changes XNAString object to XNAStringSet
xnastringClass | Development of XNAString class aims at enabling efficient manipulation of modified oligonucleotide sequences. The class consists of the following slots: name, base, sugar, backbone, target, conjugate5, conjugate3, secondary_structure, duplex_structure, dictionary (HELM-string dictionary), compl_dictionary.
xnastringClassUnions | setClassUnion definitions
xnastringElementsNumber | Function which checks if XNAString object satisfies predefined slots length
XNAStringFromHelm | Create XNAString object from HELM - user interface
XNAStringMethod | Development of XNAString class aims at enabling efficient manipulation of modified oligonucleotide sequences. The class consists of the following slots: name, base, sugar, backbone, target, conjugate5, conjugate3, secondary_structure, duplex_structure, dictionary (HELM-string dictionary), compl_dictionary.
XNAStringSet | Create class which consists of XNAString objects given as a list
XNAStringSet-class | Create class which consists of XNAString objects given as a list
XNAStringSetMethod | Create class which consists of XNAString objects given as a list
XNAStringToHelm | XNAStringToHelmFun function takes XNAString object and translates base, sugar and backbone to HELM notation
XNAVmatchPattern | This is function finding all the occurrences of a given pattern (typically short) in a (typically long) set of reference sequences.
XNAVmatchPattern-method | This is function finding all the occurrences of a given pattern (typically short) in a (typically long) set of reference sequences.
xna_dictionary | Default XNAString dictionary

## -- misc --

[-method | Create class which consists of XNAString objects given as a list
[[-method | Create class which consists of XNAString objects given as a list
[[<--method | Create class which consists of XNAString objects given as a list