XNAStringSet-class {XNAString}

R Documentation

Create class which consists of XNAString objects given as a list

Description

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.

Method to add/replace a single row (either by row index or by 'name' slot) XNAStringSet object is returned.

Usage

XNAStringSet(
  objects = NA,
  base = NA,
  sugar = NA,
  backbone = NA,
  target = NA,
  name = NA,
  conjugate3 = NA,
  conjugate5 = NA,
  col.base = "base",
  col.sugar = "sugar",
  col.backbone = "backbone",
  col.target = "target",
  col.conjugate3 = "conjugate3",
  col.conjugate5 = "conjugate5",
  col.name = "name",
  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]]

## S4 replacement method for signature 'XNAStringSet,ANY,ANY'
x[[i]] <- value

Arguments

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.
name	string (or character). In use only when objects argument is empty.
conjugate3	string (or character). In use only when objects argument is empty.
conjugate5	string (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.
col.conjugate3	character (name of target column). In use only when objects argument is empty.
col.conjugate5	character (name of target column). In use only when objects argument is empty.
col.name	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
value	XNAString object

Value

XNASTringSet object

Author(s)

Anna Gorska

Examples

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))

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