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.

Usage

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]]

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.

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

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))

[Package XNAString version 1.0.2 Index]