Efficient Manipulation of Modified Oligonucleotide Sequences

Documentation for package ‘XNAString’ version 1.0.2

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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 --

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