XNAStringSet-class {XNAString} | R Documentation |
Create class which consists of XNAString objects given as a list
Create XNAStringSet object
Define show method
Method to extract a row/rows (either by row index or by 'name' slot) XNAStringSet object is returned.
Method to extract a single row (either by row index or by 'name' slot) XNAString object is returned.
XNAStringSet( objects = NA, base = NA, sugar = NA, backbone = NA, target = NA, col.base = "base", col.sugar = "sugar", col.backbone = "backbone", col.target = "target", default_sugar = NA, default_backbone = NA, compl_dict = complementary_bases ) ## S4 method for signature 'XNAStringSet' show(object) ## S4 method for signature 'XNAStringSet,ANY,ANY,ANY' x[i] ## S4 method for signature 'XNAStringSet,ANY,ANY' x[[i]]
objects |
list of XNAString objects |
base |
string (or character), RNAString, RNAStringSet, DNAString or DNAStringSet. In use only when objects argument is empty. |
sugar |
string (or character). In use only when objects argument is empty. |
backbone |
string (or character). In use only when objects argument is empty. |
target |
DNAStringSet, DNAString or character. In use only when objects argument is empty. |
col.base |
character (name of base column). In use only when objects argument is empty. |
col.sugar |
character (name of sugar column). In use only when objects argument is empty. |
col.backbone |
character (name of backbone column). In use only when o bjects argument is empty. |
col.target |
character (name of target column). In use only when objects argument is empty. |
default_sugar |
character - only one letter. Will be replicated nchar(base) times. In use only when objects argument is empty. |
default_backbone |
character - only one letter. Will be replicated nchar(base)-1 times. In use only when objects argument is empty. |
compl_dict |
data.table with following columns: "base", "target". By default internal XNAString dictionary is used. In use only when objects argument is empty. |
object |
XNAStringSet object |
x |
XNAStringSet object |
i |
numeric, integer, character, logical - filter needed for extraction method |
XNASTringSet object
Anna Gorska
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( name = "a", base = "GGE", sugar = "FFO", backbone = "SB", dictionary = my_dic ) obj2 <- XNAString( name = "b", base = "GGE", sugar = "FFO", dictionary = my_dic ) obj3 <- XNAString( name = "b", base = c("GGE", "EEE"), sugar = c("FFO", "OOO"), dictionary = my_dic ) XNAStringSetObj <- XNAStringSet(objects = list(obj1, obj2, obj3))