XNAString-class {XNAString} | R Documentation |
The package inherits some of the functionalities from Biostrings package. In contrary to Biostrings sequences, XNAString classes allow for description of base sequence, sugar and backbone in a single object. XNAString is able to capture single stranded oligonucleotides, siRNAs, PNAs, shRNAs, gRNAs and synthetic mRNAs, and enable users to apply sequence-manipulating Bioconductor packages to their analysis. XNAString can read and write a HELM notation, compute alphabet frequency, align and match targets.
XNAString( name, base, sugar, backbone, target, conjugate5, conjugate3, secondary_structure, duplex_structure, dictionary, compl_dictionary, default_sugar, default_backbone ) ## S4 method for signature 'XNAString' show(object) ## S4 method for signature 'XNAString' initialize( .Object, name, base, sugar, backbone, target, conjugate5, conjugate3, secondary_structure, duplex_structure, dictionary, compl_dictionary, default_sugar, default_backbone ) seqtype(x) ## S4 method for signature 'XNAString' seqtype(x)
name |
string (or character) |
base |
string (or character), RNAString, RNAStringSet, DNAString or DNAStringSet |
sugar |
string (or character) |
backbone |
string (or character) |
target |
DNAStringSet, DNAString or character |
conjugate5 |
string (or character) |
conjugate3 |
string (or character) |
secondary_structure |
list |
duplex_structure |
list |
dictionary |
data.table with following columns: "HELM", "type", "symbol". By default internal XNAString dictionary is used. |
compl_dictionary |
data.table with following columns: "base", "target". By default internal XNAString dictionary is used |
default_sugar |
character, a single letter which will be replicated in sugar slot as default value |
default_backbone |
character, a single letter which will be replicated in backbone slot as default value |
object |
XNAString object |
.Object |
XNAString object |
x |
A single string specifying the type of sequences |
Object which consists of name
, base
, sugar
,
backbone
, target
, conjugate5
, conjugate3
,
secondary_structure
, duplex_structure
,
dictionary
, compl_dictionary
.
Anna Gorska
obj1 <- XNAString( base = "ATCG", sugar = "FODD", conjugate3 = "TAG" ) obj2 <- XNAString( base = "ATCG", sugar = "FODD", backbone = "SBB" ) str(obj2) name(obj2) <- 'a' base(obj2) <- 'ATTT' sugar(obj2) <- 'LMFF' backbone(obj2) <- 'BAB' conjugate5(obj2) <- 'TFJSJG' conjugate3(obj2) <- 'ARTSS' my_dic <- data.table::data.table(type = c(rep('base',3), rep('sugar',2), rep('backbone',3)), symbol = c('G', 'E', 'A', 'F', 'O', 'S', 'B', 'X')) obj1 <- XNAString(base = 'AAE', sugar = 'FFO', backbone='SB', dictionary = my_dic) obj2 <- XNAString(base = c('EAA', 'AAAA'), sugar = c('FFO', 'OOOO'), name = c('a'), conjugate5 = c('TTT'), dictionary = my_dic) my_dic <- data.table::data.table( type = c( rep("base", 3), rep("sugar", 2), rep("backbone", 3) ), symbol = c("G", "E", "A", "F", "O", "S", "B", "X") ) obj1 <- XNAString( base = "AAE", sugar = "FFO", backbone = "SB", dictionary = my_dic ) obj2 <- XNAString( base = c("EAA", "AAAA"), sugar = c("FFO", "OOOO"), name = c("a"), conjugate5 = c("TTT"), dictionary = my_dic )