| 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 |
| 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 |
| 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 |