Package 'XNAString'

Title: Efficient Manipulation of Modified Oligonucleotide Sequences
Description: The XNAString package allows for description of base sequences and associated chemical modifications in a single object. XNAString is able to capture single stranded, as well as double stranded molecules. Chemical modifications are represented as independent strings associated with different features of the molecules (base sequence, sugar sequence, backbone sequence, modifications) and can be read or written to a HELM notation. It also enables secondary structure prediction using RNAfold from ViennaRNA. XNAString is designed to be efficient representation of nucleic-acid based therapeutics, therefore it stores information about target sequences and provides interface for matching and alignment functions from Biostrings and pwalign packages.
Authors: Anna Górska [aut], Marianna Plucinska [aut, cre], Lykke Pedersen [aut], Lukasz Kielpinski [aut], Disa Tehler [aut], Peter H. Hagedorn [aut]
Maintainer: Marianna Plucinska <[email protected]>
License: GPL-2
Version: 1.15.0
Built: 2024-10-31 06:39:07 UTC
Source: https://github.com/bioc/XNAString

Help Index

XNAAlphabetFrequency returns letters frequency for a given object in base, sugar or backbone slot

Description

XNAAlphabetFrequency returns letters frequency for a given object in base, sugar or backbone slot

XNAAlphabetFrequency method returns alphabet frequency for a given object. It works for 3 slots: base, sugar and backbone. If matrix_nbr equals 1, alphabet frequency for the first elements in the slot is returned. Letters can be given as argument, otherwise unique letters in object's dictionary are in use.

Usage

XNAAlphabetFrequencyFun(
  obj,
  slot,
  letters = NA,
  matrix_nbr = 1,
  as.prob = FALSE,
  base_only = FALSE
)

XNAAlphabetFrequency(
  obj,
  slot,
  letters = NA,
  matrix_nbr = 1,
  as.prob = FALSE,
  base_only = FALSE,
  ...
)

## S4 method for signature 'XNAString'
XNAAlphabetFrequency(
  obj,
  slot,
  letters = NA,
  matrix_nbr = 1,
  as.prob = FALSE,
  base_only = FALSE
)

## S4 method for signature 'XNAStringSet'
XNAAlphabetFrequency(
  obj,
  slot,
  letters = NA,
  matrix_nbr = 1,
  as.prob = FALSE,
  base_only = FALSE
)

Arguments

obj

XNAString or XNAStringSet class
slot

string (slot name: base, sugar or backbone)
letters

character (or character vector)
matrix_nbr

numeric (1 or 2, if 1 - first slot's element is use, if 2 - 2nd element in slot)
as.prob

logical - if TRUE frequency returned as probability of occurence
base_only

logical - if TRUE, frequency checked for 'A', 'C', 'G', 'T', other
...

optional arguments to generic function to support additional methods

Value

matrix (frequency matrix for a given slot)

Examples

xnastring_obj <- XNAString(
  name = "b",
  base = c("AACC", "GGEE"),
  sugar = c("FFOO", "OODD")
)
XNAAlphabetFrequency(obj = xnastring_obj,
                     slot = "base")
XNAAlphabetFrequency(obj = xnastring_obj,
                     slot = "base",
                     as.prob = TRUE)
XNAAlphabetFrequency(obj = xnastring_obj,
                     slot = "base",
                     base_only = TRUE)
XNAAlphabetFrequency(obj = xnastring_obj,
                     slot = "base",
                     letters = c("A", "C"))
XNAAlphabetFrequency(obj = xnastring_obj,
                     slot = "base",
                     matrix_nbr = 2)

xnastring_obj_2 <- XNAString(
  base = c("ATCG"),
  sugar = c("FODD"),
  backbone = c("SBB")
)
XNAStringSet_obj <- XNAStringSet(objects = list(
  xnastring_obj,
  xnastring_obj_2
))
XNAAlphabetFrequency(XNAStringSet_obj, "sugar")

Backbone setter/getter method

Description

Getter methods enable extraction of single slots from XNAString and XNAStringSet objects. E.g. name method extracts name slot from XNAString/XNAStringSet object.

Usage

backbone(x, ...)

## S4 method for signature 'XNAString'
backbone(x)

## S4 method for signature 'XNAStringSet'
backbone(x, i = 1)

backbone(x, ...) <- value

## S4 replacement method for signature 'XNAString'
backbone(x) <- value

## S4 replacement method for signature 'XNAStringSet'
backbone(x, i = 1) <- value

Arguments

x

XNAString/XNAStringSet object
...

optional arguments to generic function to support additional methods
i

numeric - possibilities: 1 or 2. If 1 - 1st slots elements printed out, 2nd otherwise. In case the second element is not in the object, empty char created. This parameter is only available for XNAStringSet objects.
value

character vector applied only for setter method

Details

Setter methods enable overwriting single slots from XNAString and XNAStringSet objects. E.g. name<- method overwrites existing name slot

Value

vector in getter method, XNAStringSet object (with replaced name slot) in setter method

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")
)
obj <- XNAString(
  name = "b",
  base = "GGE",
  sugar = "FFO",
  dictionary = my_dic
)
backbone(obj)

Base setter/getter method

Description

Getter methods enable extraction of single slots from XNAString and XNAStringSet objects. E.g. name method extracts name slot from XNAString/XNAStringSet object.

Usage

base(x, ...)

## S4 method for signature 'XNAString'
base(x)

## S4 method for signature 'XNAStringSet'
base(x, i = 1)

base(x, ...) <- value

## S4 replacement method for signature 'XNAString'
base(x) <- value

## S4 replacement method for signature 'XNAStringSet'
base(x, i = 1) <- value

Arguments

x

XNAString/XNAStringSet object
...

optional arguments to generic function to support additional methods
i

numeric - possibilities: 1 or 2. If 1 - 1st slots elements printed out, 2nd otherwise. In case the second element is not in the object, empty char created. This parameter is only available for XNAStringSet objects.
value

character vector applied only for setter method

Details

Setter methods enable overwriting single slots from XNAString and XNAStringSet objects. E.g. name<- method overwrites existing name slot

Value

vector in getter method, XNAStringSet object (with replaced name slot) in setter method

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")
)
obj <- XNAString(
  name = "b",
  base = "GGE",
  sugar = "FFO",
  dictionary = my_dic
)
base(obj)

Translate base slot based on complementary bases dictionary. Base sequence in transformed using compl_target column.

Description

Translate base slot based on complementary bases dictionary. Base sequence in transformed using compl_target column.

Usage

changeBase(compl_dict, bases)

Arguments

compl_dict

complementary bases dictionary
bases

string, one or two-elements vector

Value

string

Compl_dictionary setter/getter method

Description

Getter methods enable extraction of single slots from XNAString and XNAStringSet objects. E.g. name method extracts name slot from XNAString/XNAStringSet object.

Usage

compl_dictionary(x, ...)

## S4 method for signature 'XNAString'
compl_dictionary(x)

compl_dictionary(x, ...) <- value

## S4 replacement method for signature 'XNAString'
compl_dictionary(x) <- value

Arguments

x

XNAString/XNAStringSet object
...

optional arguments to generic function to support additional methods
value

character vector applied only for setter method

Details

Setter methods enable overwriting single slots from XNAString and XNAStringSet objects. E.g. name<- method overwrites existing name slot

Value

vector in getter method, XNAStringSet object (with replaced name slot) in setter method

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")
)
obj <- XNAString(
  name = "b",
  base = "GGE",
  sugar = "FFO",
  dictionary = my_dic
)
compl_dictionary(obj)

Default XNAString complementarity dictionary

Description

A dataset containing default internal XNAString dictionary with base complemetary.

Usage

data(complementary_bases)

Format

A data.table with 6 rows and 3 variables:

base

base symbol

target

complementary base

compl_target

complementary target

Source

RMR internal bioinformatics database (Mimir)

Concatenate HELM-symbol custom dictionary with built-in HELM-symbol dictionary (xna_dictionary)

Description

Concatenate HELM-symbol custom dictionary with built-in HELM-symbol dictionary (xna_dictionary)

Usage

concatDict(
  custom_dict,
  default_dict = xna_dictionary,
  helm_colname = "HELM",
  type_colname = "type",
  symbol_colname = "symbol"
)

Arguments

custom_dict

custom HELM-symbol dictionary
default_dict

built-in HELM-symbol dictionary (xna_dictionary)
helm_colname

helm column name in custom dictionary
type_colname

type column name in custom dictionary
symbol_colname

symbol column name in custom dictionary

Value

data.table

Examples

my_dict <- data.table::data.table(
  HELM = c("[[B]]"),
  type = c("base"),
  symbol = c("B")
)
concatDict(my_dict)

Conjugate3 setter/getter method

Description

Getter methods enable extraction of single slots from XNAString and XNAStringSet objects. E.g. name method extracts name slot from XNAString/XNAStringSet object.

Usage

conjugate3(x, ...)

## S4 method for signature 'XNAString'
conjugate3(x)

## S4 method for signature 'XNAStringSet'
conjugate3(x, i = 1)

conjugate3(x, ...) <- value

## S4 replacement method for signature 'XNAString'
conjugate3(x) <- value

## S4 replacement method for signature 'XNAStringSet'
conjugate3(x, i = 1) <- value

Arguments

x

XNAString/XNAStringSet object
...

optional arguments to generic function to support additional methods
i

numeric - possibilities: 1 or 2. If 1 - 1st slots elements printed out, 2nd otherwise. In case the second element is not in the object, empty char created. This parameter is only available for XNAStringSet objects.
value

character vector applied only for setter method

Details

Setter methods enable overwriting single slots from XNAString and XNAStringSet objects. E.g. name<- method overwrites existing name slot

Value

vector in getter method, XNAStringSet object (with replaced name slot) in setter method

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")
)
obj <- XNAString(
  name = "b",
  base = "GGE",
  sugar = "FFO",
  dictionary = my_dic
)
conjugate3(obj)

Conjugate5 setter/getter method

Description

Getter methods enable extraction of single slots from XNAString and XNAStringSet objects. E.g. name method extracts name slot from XNAString/XNAStringSet object.

Usage

conjugate5(x, ...)

## S4 method for signature 'XNAString'
conjugate5(x)

## S4 method for signature 'XNAStringSet'
conjugate5(x, i = 1)

conjugate5(x, ...) <- value

## S4 replacement method for signature 'XNAString'
conjugate5(x) <- value

## S4 replacement method for signature 'XNAStringSet'
conjugate5(x, i = 1) <- value

Arguments

x

XNAString/XNAStringSet object
...

optional arguments to generic function to support additional methods
i

numeric - possibilities: 1 or 2. If 1 - 1st slots elements printed out, 2nd otherwise. In case the second element is not in the object, empty char created. This parameter is only available for XNAStringSet objects.
value

character vector applied only for setter method

Details

Setter methods enable overwriting single slots from XNAString and XNAStringSet objects. E.g. name<- method overwrites existing name slot

Value

vector in getter method, XNAStringSet object (with replaced name slot) in setter method

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")
)
obj <- XNAString(
  name = "b",
  base = "GGE",
  sugar = "FFO",
  dictionary = my_dic
)
conjugate5(obj)

Default_backbone setter/getter method

Description

Getter methods enable extraction of single slots from XNAString and XNAStringSet objects. E.g. name method extracts name slot from XNAString/XNAStringSet object.

Usage

default_backbone(x, ...)

## S4 method for signature 'XNAString'
default_backbone(x)

## S4 method for signature 'XNAStringSet'
default_backbone(x)

default_backbone(x, ...) <- value

## S4 replacement method for signature 'XNAString'
default_backbone(x) <- value

Arguments

x

XNAString/XNAStringSet object
...

optional arguments to generic function to support additional methods
value

character vector applied only for setter method

Details

Setter methods enable overwriting single slots from XNAString and XNAStringSet objects. E.g. name<- method overwrites existing name slot

Value

vector in getter method, XNAStringSet object (with replaced name slot) in setter method

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")
)
obj <- XNAString(
  name = "b",
  base = "GGE",
  default_sugar = 'F',
  default_backbone = 'X',
  dictionary = my_dic
)
default_backbone(obj)

Default_sugar setter/getter method

Description

Getter methods enable extraction of single slots from XNAString and XNAStringSet objects. E.g. name method extracts name slot from XNAString/XNAStringSet object.

Usage

default_sugar(x, ...)

## S4 method for signature 'XNAString'
default_sugar(x)

## S4 method for signature 'XNAStringSet'
default_sugar(x)

default_sugar(x, ...) <- value

## S4 replacement method for signature 'XNAString'
default_sugar(x) <- value

Arguments

x

XNAString/XNAStringSet object
...

optional arguments to generic function to support additional methods
value

character vector applied only for setter method

Details

Setter methods enable overwriting single slots from XNAString and XNAStringSet objects. E.g. name<- method overwrites existing name slot

Value

vector in getter method, XNAStringSet object (with replaced name slot) in setter method

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")
)
obj <- XNAString(
  name = "b",
  base = "GGE",
  default_sugar = 'F',
  default_backbone = 'X',
  dictionary = my_dic
)
default_sugar(obj)

Dictionary setter/getter method

Description

Getter methods enable extraction of single slots from XNAString and XNAStringSet objects. E.g. name method extracts name slot from XNAString/XNAStringSet object.

Usage

dictionary(x, ...)

## S4 method for signature 'XNAString'
dictionary(x)

dictionary(x, ...) <- value

## S4 replacement method for signature 'XNAString'
dictionary(x) <- value

Arguments

x

XNAString/XNAStringSet object
...

optional arguments to generic function to support additional methods
value

character vector applied only for setter method

Details

Setter methods enable overwriting single slots from XNAString and XNAStringSet objects. E.g. name<- method overwrites existing name slot

Value

vector in getter method, XNAStringSet object (with replaced name slot) in setter method

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")
)
obj <- XNAString(
  name = "b",
  base = "GGE",
  sugar = "FFO",
  dictionary = my_dic
)
dictionary(obj)

XNADinucleotideFrequencyFun returns double letters frequency for a given object in base, sugar or backbone slot

Description

XNADinucleotideFrequencyFun returns double letters frequency for a given object in base, sugar or backbone slot

XNADinucleotideFrequency method returns dinucleotide frequency for a given object. It works for 3 slots: base, sugar and backbone. If matrix_nbr equals 1, dinucleotide frequency for the first elements in the slot is returned. Double letters can be given as argument, otherwise unique double letters in object's dictionary are in use.

Usage

XNADinucleotideFrequencyFun(
  obj,
  slot,
  double_letters = NA,
  matrix_nbr = 1,
  as.prob = FALSE,
  base_only = FALSE
)

XNADinucleotideFrequency(
  obj,
  slot,
  double_letters = NA,
  matrix_nbr = 1,
  as.prob = FALSE,
  base_only = FALSE,
  ...
)

## S4 method for signature 'XNAString'
XNADinucleotideFrequency(
  obj,
  slot,
  double_letters = NA,
  matrix_nbr = 1,
  as.prob = FALSE,
  base_only = FALSE
)

## S4 method for signature 'XNAStringSet'
XNADinucleotideFrequency(
  obj,
  slot,
  double_letters = NA,
  matrix_nbr = 1,
  as.prob = FALSE,
  base_only = FALSE
)

Arguments

obj

XNAString or XNAStringSet class
slot

string (slot name: base, sugar or backbone)
double_letters

string (or string vector) - double letters
matrix_nbr

numeric (1 or 2, if 1 - first slot's element is use, if 2 - 2nd element in slot)
as.prob

logical - if TRUE frequency returned as probability of occurence
base_only

logical - if TRUE, frequency checked for 'A', 'C', 'G', 'T', other
...

optional arguments to generic function to support additional methods

Value

matrix (frequency matrix for a given slot)

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")
)
xnastring_obj <- XNAString(
 name = "b",
 base = c("GGEG"),
 sugar = c("FFOO"),
 dictionary = my_dic
)
XNAString::XNADinucleotideFrequency(
 obj = xnastring_obj,
 slot = "base",
 matrix_nbr = 1
)

Function which creates XNAstringSet object from table with base, sugar and backbone columns.

Description

Function which creates XNAstringSet object from table with base, sugar and backbone columns.

Usage

dt2Set(
  table,
  col.base = "base",
  col.sugar = "sugar",
  col.backbone = "backbone",
  col.target = "target",
  default_sugar = NA,
  default_backbone = NA,
  compl_dict = complementary_bases
)

Arguments

table

data.table or data.frame (must incluse base, sugar and backbone columns)
col.base

character (name of base column)
col.sugar

character (name of sugar column)
col.backbone

character (name of backbone column)
col.target

character (name of target column)
default_sugar

character - only one letter. Will be replicated nchar(base) times
default_backbone

character - only one letter. Will be replicated nchar(base)-1 times
compl_dict

data.table with following columns: "base", "target". By default internal XNAString dictionary is used

Value

XNAStringSet object

Examples

dt <- data.table::data.table(
  base = c("TT", "GG"),
  sugar = c("FF", "FO"),
  backbone = c("S", "S")
)
dt2Set(dt)

Duplex_structure setter/getter method

Description

Getter methods enable extraction of single slots from XNAString and XNAStringSet objects. E.g. name method extracts name slot from XNAString/XNAStringSet object.

Usage

duplex_structure(x, ...)

## S4 method for signature 'XNAString'
duplex_structure(x)

## S4 method for signature 'XNAStringSet'
duplex_structure(x)

duplex_structure(x, ...) <- value

## S4 replacement method for signature 'XNAString'
duplex_structure(x) <- value

Arguments

x

XNAString/XNAStringSet object
...

optional arguments to generic function to support additional methods
value

character vector applied only for setter method

Details

Setter methods enable overwriting single slots from XNAString and XNAStringSet objects. E.g. name<- method overwrites existing name slot

Value

vector in getter method, XNAStringSet object (with replaced name slot) in setter method

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")
)
obj <- XNAString(
  name = "b",
  base = "GGE",
  sugar = "FFO",
  dictionary = my_dic
)
duplex_structure(obj)

Translate RNA from HELM notation to multi-string notation

Description

This function translates RNA molecules encoded in HELM notation into multi-string notation. It uses dictionary which links HELM code for base, sugar and backbone elements with symbols used in multi-string notation.

Usage

helm2String(helm, dictionary = xna_dictionary, remove_linker = TRUE)

Arguments

helm

string with HELM sequence, which contains one RNA polymer and optionally CHEM element
dictionary

data.table with following columns: "HELM", "type", "symbol". By default internal XNAString dictionary is used.
remove_linker

logical defines if linker should be clipped from RNA

Value

named list of strings with following elements: base, sugar, backbone, conjugate5, conjugate3

Author(s)

Marianna Plucinska

Examples

helm2String("RNA1{[dR](A)P.[dR](A)P.[dR](A)}$$$$V2.0")

Check on an object type

Description

Check on an object type

Usage

instanceOf(object, type)

Arguments

object

an object of any class
type

class of an object

Value

logical information. TRUE if object class equals type

Examples

instanceOf(1, "numeric")

Save list of lists as data.table

Description

Save list of lists as data.table

Usage

listOflists2Dt(list_of_lists)

Arguments

list_of_lists

list of lists that will be saved as data.table.

Value

data.table

Examples

nested_list <- list(
  list(base = c("T"), sugar = c("G")),
  list(base = c("U"), sugar = c("G"))
)
listOflists2Dt(nested_list)

Reformat mimir table to XNA dictionary standards

Description

Reformat mimir table to XNA dictionary standards

Usage

mimir2XnaDict(table, base.col, sugar.col, backbone.col)

Arguments

table

data.table or data.frame (must incluse "HELM", "TS_BASE_SEQ", "TS_SUGAR_SEQ" and "TS_BACKBONE_SEQ" columns)
base.col

character (base column name)
sugar.col

character (sugar column name)
backbone.col

character (backbone column name)

Value

data.table (written in the xna_dictionary format)

Examples

dt <- data.table::data.table(HELM = c("([PPG])", "[fR]", "[srP]"),
                 TS_BASE_SEQ = c("F", NA, NA),
                 TS_SUGAR_SEQ = c(NA, NA, 'F'),
                 TS_BACKBONE_SEQ = c(NA, 'S', NA))
mimir2XnaDict(dt, 'TS_BASE_SEQ', 'TS_SUGAR_SEQ', 'TS_BACKBONE_SEQ')

Name setter/getter method

Description

Getter methods enable extraction of single slots from XNAString and XNAStringSet objects. E.g. name method extracts name slot from XNAString/XNAStringSet object.

Usage

name(x, ...)

## S4 method for signature 'XNAString'
name(x)

## S4 method for signature 'XNAStringSet'
name(x, i = 1)

name(x, ...) <- value

## S4 replacement method for signature 'XNAString'
name(x) <- value

## S4 replacement method for signature 'XNAStringSet'
name(x, i = 1) <- value

Arguments

x

XNAString/XNAStringSet object
...

optional arguments to generic function to support additional methods
i

numeric - possibilities: 1 or 2. If 1 - 1st slots elements printed out, 2nd otherwise. In case the second element is not in the object, empty char created. This parameter is only available for XNAStringSet objects.
value

character vector applied only for setter method

Details

Setter methods enable overwriting single slots from XNAString and XNAStringSet objects. E.g. name<- method overwrites existing name slot

Value

vector in getter method, XNAStringSet object (with replaced name slot) in setter method

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")
)
obj <- XNAString(
  name = "b",
  base = "GGE",
  sugar = "FFO",
  dictionary = my_dic
)
name(obj)
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 = "b",
  base = "GGE",
  sugar = "FFO",
  dictionary = my_dic
)
obj2 <- XNAString(
  name = "b",
  base = c("GGE", "EEE"),
  sugar = c("FFO", "OOO"),
  dictionary = my_dic
)
XNAStringSetObj <- XNAStringSet(objects = list(obj1, obj2))
name(XNAStringSetObj)
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")
)
obj <- XNAString(
  name = "b",
  base = "GGE",
  sugar = "FFO",
  dictionary = my_dic
)
name(obj) <- "new_name"
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 = "b",
  base = "GGE",
  sugar = "FFO",
  dictionary = my_dic
)
obj2 <- XNAString(
  name = "b",
  base = c("GGE", "EEE"),
  sugar = c("FFO", "OOO"),
  dictionary = my_dic
)
XNAStringSetObj <- XNAStringSet(objects = list(obj1, obj2))
name(XNAStringSetObj, 1) <- c("new1", "new2")

Objects getter method for XNAStringSet class

Description

Getter methods enable extraction of single slots from XNAStringSet objects. E.g. objects method extracts objects slot from XNAStringSet object. It is a list of XNAString objects.

Usage

objects(x, ...)

## S4 method for signature 'XNAStringSet'
objects(x)

Arguments

x

XNAStringSet object
...

optional arguments to generic function to support additional methods

Value

list of XNAString objects

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'))
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(obj2, obj3))
objects(XNAStringSetObj)

Parse monomers from HELM to multi-string notation

Description

Parse monomers from HELM to multi-string notation

Usage

parseRnaHelmComponent(rna_component, dictionary = xna_dictionary)

Arguments

rna_component

list of monomers building RNA
dictionary

data.table with following columns: "HELM", "type", "symbol". By default internal XNAString dictionary is used.

Value

list of three strings: base, sugar, backbone

Author(s)

Marianna Plucinska

Examples

parseRnaHelmComponent(c("[dR](A)P", "[dR](A)P", "[dR](A)"))

Compute Minimum Free Energy (MFE), and a corresponding secondary structure for two dimerized RNA sequences.

Description

This function is a wrapper for RNAcofold from ViennaRNA package.

Usage

predictDuplexStructureFun(obj)

predictDuplexStructure(obj, ...)

## S4 method for signature 'XNAString'
predictDuplexStructure(obj)

Arguments

obj

XNAString object
...

optional arguments to generic function to support additional methods

Value

list (structure and mfe)

Examples

obj1 <- XNAString(
  base = "ATCG",
  sugar = "FODD",
  conjugate3 = "TAG"
)
predictDuplexStructure(obj1)

Prediction of MFE structure with ViennaRNA package

Description

This function is a wrapper for RNAfold from ViennaRNA package.

Usage

predictMfeStructureFun(obj)

predictMfeStructure(obj, ...)

## S4 method for signature 'XNAString'
predictMfeStructure(obj)

Arguments

obj

XNAString object
...

optional arguments to generic function to support additional methods

Value

character, secondary structure in dot-bracket notation

Examples

obj1 <- XNAString(
  base = "ATCG",
  sugar = "FODD",
  conjugate3 = "TAG"
)
predictMfeStructure(obj1)

Reverse complement sequence based on dictionary

Description

Reverse complement sequence based on dictionary

Usage

reverseComplementFun(obj)

Arguments

obj

XNAString object

Value

string with reverse complement sequence

Secondary_structure setter/getter method

Description

Getter methods enable extraction of single slots from XNAString and XNAStringSet objects. E.g. name method extracts name slot from XNAString/XNAStringSet object.

Usage

secondary_structure(x, ...)

## S4 method for signature 'XNAString'
secondary_structure(x)

## S4 method for signature 'XNAStringSet'
secondary_structure(x)

secondary_structure(x, ...) <- value

## S4 replacement method for signature 'XNAString'
secondary_structure(x) <- value

Arguments

x

XNAString/XNAStringSet object
...

optional arguments to generic function to support additional methods
value

character vector applied only for setter method

Details

Setter methods enable overwriting single slots from XNAString and XNAStringSet objects. E.g. name<- method overwrites existing name slot

Value

vector in getter method, XNAStringSet object (with replaced name slot) in setter method

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")
)
obj <- XNAString(
  name = "b",
  base = "GGE",
  sugar = "FFO",
  dictionary = my_dic
)
secondary_structure(obj)

Create set of functions and methods to calculate alphabet frequency in base, sugar and backbone slots

Description

Create set of functions and methods to calculate alphabet frequency in base, sugar and backbone slots

Usage

seqAlphabetFrequency(unique_letters, seq, as.prob)

Arguments

unique_letters

string (or character) - these letters pose column names
seq

string (or character) - frequency is calculated for this string
as.prob

logical - if TRUE frequency returned as probability of occurrence

Value

numeric - named numeric vector

Examples

seqAlphabetFrequency(c("A", "B", "C"), c("AABA"), as.prob = FALSE)

Create set of functions and methods to calculate dinucleotide frequency in base, sugar and backbone slots

Description

Create set of functions and methods to calculate dinucleotide frequency in base, sugar and backbone slots

Usage

seqDinucleotideFrequency(unique_sets, seq, as.prob)

Arguments

unique_sets

string vector of double letters -these letters pose column names
seq

string (or character) - frequency is calculated for this string
as.prob

logical - if TRUE frequency returned as probability of occurrence

Value

numeric - named numeric vector

Examples

seqDinucleotideFrequency(c("AB", "BA", "CD"),
                                   "ABABAB",
                                    as.prob = FALSE)
seqDinucleotideFrequency(c("GC", "CG", "CC"),
                         "GCCG",
                         as.prob = FALSE)

seqVectorAlphabetFrequency function calculates frequency for strings vector

Description

seqVectorAlphabetFrequency function calculates frequency for strings vector

Usage

seqVectorAlphabetFrequency(unique_letters, seq_vec, as.prob)

Arguments

unique_letters

string (or character) - these letters pose column names
seq_vec

vector of strings (or characters) - frequency will be calculated for this vector
as.prob

logical - if TRUE frequency returned as probability of occurence

Value

matrix - each row denotes frequency for a specific string of vector

Examples

seqVectorAlphabetFrequency(c("A", "B", "C"),
  c("AABA", "BBBCCC"),
  as.prob = FALSE
)

seqVectorDinucleotideFrequency function calculates frequency for strings vector

Description

seqVectorDinucleotideFrequency function calculates frequency for strings vector

Usage

seqVectorDinucleotideFrequency(unique_sets, seq_vec, as.prob)

Arguments

unique_sets

string vector of double letters -these letters pose column names
seq_vec

vector of strings (or characters) - frequency will be calculated for this vector
as.prob

logical - if TRUE frequency returned as probability of occurence

Value

matrix - each row denotes frequency for a specific string of vector

Examples

seqVectorDinucleotideFrequency(c("AB", "BA", "CD"),
                                         c("ABABAB", "ABABCD"),
                                         as.prob = FALSE)

set2Dt function - changes XNAStringSet object to data.table

Description

set2Dt function - changes XNAStringSet object to data.table

Usage

set2Dt(obj, slots)

Arguments

obj

XNAStringSet object
slots

slots that are saved as column names (possibilities: "name", "base", "sugar", "backbone", "target", "conjugate5", "conjugate3" and "dictionary" )

Value

data.table

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'))
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(obj2, obj3))
set2Dt(XNAStringSetObj, c('base', 'sugar'))

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")
)
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(obj2, obj3))
set2Dt(XNAStringSetObj, c("base", "sugar"))

Define method to save XNAStringSet object as a list of XNAString objects

Description

Define method to save XNAStringSet object as a list of XNAString objects

Usage

set2List(obj)

## S4 method for signature 'XNAStringSet'
set2List(obj)

Arguments

obj

XNAStringSet object

Value

list of XNAString objects

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'))
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(obj2, obj3))
set2List(XNAStringSetObj)

siRNA_HELM function takes XNAString object and returns pairing information for base slot. Works only for double stranded molecules.

Description

siRNA_HELM function takes XNAString object and returns pairing information for base slot. Works only for double stranded molecules.

Usage

siRNA_HELM(xnastring_obj)

Arguments

xnastring_obj

XNAString object

Value

string

Examples

obj1 <- XNAString(
  base = c("CCCCUGCCGUGGUUCAUAA", "UUAUGAACCACGGCAGGGGCG"),
  sugar = c("OOFOFOFOFOFOFOFOFOF", "FFOFOFOFOFOFOFOFOFOFO"),
  backbone = c("OOOOOOOOOOOOOOOOOO", "OOOOOOOOOOOOOOOOOOOO"),
  conjugate3 = c("")
)

siRNA_HELM(obj1)

Sugar setter/getter method

Description

Getter methods enable extraction of single slots from XNAString and XNAStringSet objects. E.g. name method extracts name slot from XNAString/XNAStringSet object.

Usage

sugar(x, ...)

## S4 method for signature 'XNAString'
sugar(x)

## S4 method for signature 'XNAStringSet'
sugar(x, i = 1)

sugar(x, ...) <- value

## S4 replacement method for signature 'XNAString'
sugar(x) <- value

## S4 replacement method for signature 'XNAStringSet'
sugar(x, i = 1) <- value

Arguments

x

XNAString/XNAStringSet object
...

optional arguments to generic function to support additional methods
i

numeric - possibilities: 1 or 2. If 1 - 1st slots elements printed out, 2nd otherwise. In case the second element is not in the object, empty char created. This parameter is only available for XNAStringSet objects.
value

character vector applied only for setter method

Details

Setter methods enable overwriting single slots from XNAString and XNAStringSet objects. E.g. name<- method overwrites existing name slot

Value

vector in getter method, XNAStringSet object (with replaced name slot) in setter method

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")
)
obj <- XNAString(
  name = "b",
  base = "GGE",
  sugar = "FFO",
  dictionary = my_dic
)
sugar(obj)

Target setter/getter method

Description

Getter methods enable extraction of single slots from XNAString and XNAStringSet objects. E.g. name method extracts name slot from XNAString/XNAStringSet object.

Usage

target(x, ...)

## S4 method for signature 'XNAString'
target(x)

## S4 method for signature 'XNAStringSet'
target(x, i = 1)

target(x, ...) <- value

## S4 replacement method for signature 'XNAString'
target(x) <- value

## S4 replacement method for signature 'XNAStringSet'
target(x, i = 1) <- value

Arguments

x

XNAString/XNAStringSet object
...

optional arguments to generic function to support additional methods
i

numeric - possibilities: 1 or 2. If 1 - 1st slots elements printed out, 2nd otherwise. In case the second element is not in the object, empty char created. This parameter is only available for XNAStringSet objects.
value

character vector applied only for setter method

Details

Setter methods enable overwriting single slots from XNAString and XNAStringSet objects. E.g. name<- method overwrites existing name slot

Value

vector in getter method, XNAStringSet object (with replaced name slot) in setter method

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")
)
obj <- XNAString(
  name = "b",
  base = "GGE",
  sugar = "FFO",
  dictionary = my_dic
)
target(obj)

Check if all objects are of XNAString class and dictionaries are the same

Description

Check if all objects are of XNAString class and dictionaries are the same

Usage

typedListCheck(object)

Arguments

object

an object of any class. An object must contain 'objects' (list type) slot

Value

logical information. Checks the whole list of objects, TRUE if class of all objects equals 'XNAString' and their dictionaries are the same.

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")
)
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(obj2, obj3))
typedListCheck(XNAStringSetObj)

Utility functions useful when programming and developing XNAString class

Description

Utility functions useful when programming and developing XNAString class

Usage

uniqueChars(x)

Arguments

x

A string vector

Value

A list of vectors with unique characters found in x string

Examples

uniqueChars("TRGFFTR")
uniqueChars(c("TRGFFTR", "AATGRC"))

Default XNAString dictionary

Description

A dataset containing default internal XNAString dictionary with HELM to string translation.

Usage

data(xna_dictionary)

Format

A data.table with 20 rows and 3 variables:

HELM

HELM sequence coding monomer

type

if element is coding base, sugar, backbone

symbol

single string translation of HELM

Source

RMR internal bioinformatics database (Mimir)

Finds pattern in reference sequence

Description

This is function finding all the occurrences of a given pattern (typically short) in a (typically long) reference sequence

Usage

XNAMatchPattern(
  pattern,
  subject,
  target.number = 1,
  max.mismatch = 0,
  min.mismatch = 0,
  with.indels = FALSE,
  fixed = TRUE,
  algorithm = "auto"
)

## S4 method for signature 'XNAString,character'
XNAMatchPattern(
  pattern,
  subject,
  target.number = 1,
  max.mismatch = 0,
  min.mismatch = 0,
  with.indels = FALSE,
  fixed = TRUE,
  algorithm = "auto"
)

## S4 method for signature 'XNAString,XString'
XNAMatchPattern(
  pattern,
  subject,
  target.number = 1,
  max.mismatch = 0,
  min.mismatch = 0,
  with.indels = FALSE,
  fixed = TRUE,
  algorithm = "auto"
)

Arguments

pattern

XNAString object with non-empty target slot
subject

string or DNAString object
target.number

numeric - if target is a multi-element vector, then specify which element in use. 1 is the default
max.mismatch

The maximum number of mismatching letters allowed. If non-zero, an algorithm that supports inexact matching is used.
min.mismatch

The minimum number of mismatching letters allowed. If non-zero, an algorithm that supports inexact matching is used.
with.indels

If TRUE then indels are allowed. In that case, min.mismatch must be 0 and max.mismatch is interpreted as the maximum "edit distance" allowed between the pattern and a match. Note that in order to avoid pollution by redundant matches, only the "best local matches" are returned. Roughly speaking, a "best local match" is a match that is locally both the closest (to the pattern P) and the shortest.
fixed

If TRUE (the default), an IUPAC ambiguity code in the pattern can only match the same code in the subject, and vice versa. If FALSE, an IUPAC ambiguity code in the pattern can match any letter in the subject that is associated with the code, and vice versa.
algorithm

One of the following: "auto", "naive-exact", "naive-inexact", "boyer-moore", "shift-or" or "indels".

Value

an XStringViews object for matchPattern.

Examples

s1 <-
XNAString::XNAString(
 base = Biostrings::DNAString("GCGGAGAGAGCACAGATACA"),
 sugar = "FODDDDDDDDDDDDDDDDDD",
 target = Biostrings::DNAStringSet("GGCGGAGAGAGCACAGATACA")
)
XNAString::XNAMatchPattern(
s1,
"GGCGGAGAGAGCACAGATACAGGCGGAGAGAGCACAGATACA"
)

Find set of patterns in reference sequence

Description

This is function finding all the occurrences of a given set of patterns (typically short) in a (typically long) reference sequence

Usage

XNAMatchPDict(
  pdict,
  subject,
  max.mismatch = 0,
  min.mismatch = 0,
  with.indels = FALSE,
  fixed = TRUE,
  algorithm = "auto",
  verbose = FALSE
)

## S4 method for signature 'XNAString,character'
XNAMatchPDict(
  pdict,
  subject,
  max.mismatch = 0,
  min.mismatch = 0,
  with.indels = FALSE,
  fixed = TRUE,
  algorithm = "auto",
  verbose = FALSE
)

## S4 method for signature 'XNAString,XString'
XNAMatchPDict(
  pdict,
  subject,
  max.mismatch = 0,
  min.mismatch = 0,
  with.indels = FALSE,
  fixed = TRUE,
  algorithm = "auto",
  verbose = FALSE
)

Arguments

pdict

XNAString object, target slot taken as pdict object from Biostrings
subject

string containing sequence
max.mismatch

The maximum number of mismatching letters allowed. If non-zero, an algorithm that supports inexact matching is used.
min.mismatch

The minimum number of mismatching letters allowed. If non-zero, an algorithm that supports inexact matching is used.
with.indels

If TRUE then indels are allowed. In that case, min.mismatch must be 0 and max.mismatch is interpreted as the maximum "edit distance" allowed between the pattern and a match. Note that in order to avoid pollution by redundant matches, only the "best local matches" are returned. Roughly speaking, a "best local match" is a match that is locally both the closest (to the pattern P) and the shortest.
fixed

If TRUE (the default), an IUPAC ambiguity code in the pattern can only match the same code in the subject, and vice versa. If FALSE, an IUPAC ambiguity code in the pattern can match any letter in the subject that is associated with the code, and vice versa.
algorithm

One of the following: "auto", "naive-exact", "naive-inexact", "boyer-moore", "shift-or" or "indels".
verbose

TRUE or FALSE.

Value

an MIndex object of length M, and countPDict an integer vector of length M.

Examples

s2 <-
XNAString::XNAString(
 base = "GCGGAGAGAGCACAGATACA",
 sugar = "FODDDDDDDDDDDDDDDDDD",
 target = Biostrings::DNAStringSet(c(
   "GGCGGAGAGAGCACAGATACA", "GGCGGAGAGAGCACAGATACA"
 ))
)
o <- XNAString::XNAMatchPDict(
 s2,
 "GGCGGAGAGAGCACAGATACAGGGGCGGAGAGAGCACAGATACACGGAGAGAGCACAGATACA"
)

xnaObj2Dt function - changes XNAString object to data.table

Description

xnaObj2Dt function - changes XNAString object to data.table

Usage

xnaObj2Dt(obj, slots)

Arguments

obj

XNAString object
slots

slots that are saved as column names (possibilities: "name", "base", "sugar", "backbone", "target", "conjugate5", "conjugate3" and "dictionary" )

Value

data.table

Pairwise alignment methods for XNAString object

Description

This function performs pairwise alignment for sequences stored in target slot of XNAString object with subject

Usage

XNAPairwiseAlignment(pattern, subject, ...)

## S4 method for signature 'XNAString,character'
XNAPairwiseAlignment(
  pattern,
  subject,
  type = "global",
  substitutionMatrix = NULL,
  fuzzyMatrix = NULL,
  gapOpening = 10,
  gapExtension = 4,
  scoreOnly = FALSE
)

Arguments

pattern

XNAString object, pattern taken from target slot.
subject

a character vector of length 1, an XString, or an XStringSet object of length 1.
...

optional arguments to generic function to support additional methods
type

type of alignment. One of "global", "local", "overlap", "global-local", and "local-global" where "global" = align whole strings with end gap penalties, "local" = align string fragments, "overlap" = align whole strings without end gap penalties, "global-local" = align whole strings in pattern with consecutive subsequence of subject, "local-global" = align consecutive subsequence of pattern with whole strings in subject.
substitutionMatrix

substitution matrix representing the fixed substitution scores for an alignment. It cannot be used in conjunction with patternQuality and subjectQuality arguments.
fuzzyMatrix

fuzzy match matrix for quality-based alignments. It takes values between 0 and 1; where 0 is an unambiguous mismatch, 1 is an unambiguous match, and values in between represent a fraction of "matchiness".
gapOpening

the cost for opening a gap in the alignment.
gapExtension

the incremental cost incurred along the length of the gap in the alignment.
scoreOnly

logical to denote whether or not to return just the scores of the optimal pairwise alignment.

Value

an instance of class PairwiseAlignments

Examples

mat <-
 pwalign::nucleotideSubstitutionMatrix(
   match = 1,
   mismatch = -3,
   baseOnly = TRUE
)
s1 <-
  XNAString::XNAString(
    base = "GCGGAGAGAGCACAGATACA",
    sugar = "FODDDDDDDDDDDDDDDDDD",
    target = Biostrings::DNAStringSet("GGCGGAGAGAGCACAGATACA")
  )
  
  XNAString::XNAPairwiseAlignment(s1,
                                  "ACCCACACACACACACACACAC",
                                  "global",
                                  substitutionMatrix = mat
  )

Reverse complement sequence based on dictionary

Description

Reverse complement sequence based on dictionary

Usage

XNAReverseComplement(obj, ...)

## S4 method for signature 'XNAString'
XNAReverseComplement(obj)

Arguments

obj

XNAString object
...

optional arguments to generic function to support additional methods

Value

string with reverse complement sequence

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")
)
obj <- XNAString(
  name = "b",
  base = "GGE",
  sugar = "FFO",
  dictionary = my_dic
)
XNAReverseComplement(obj)

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.

Description

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.

Usage

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)

Arguments

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

Value

Object which consists of name, base, sugar, backbone, target, conjugate5, conjugate3, secondary_structure, duplex_structure, dictionary, compl_dictionary.

Author(s)

Anna Gorska

Examples

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
)

XNAString2XNAStringSet function - changes XNAString object to XNAStringSet

Description

XNAString2XNAStringSet function - changes XNAString object to XNAStringSet

Usage

XNAString2XNAStringSet(XNAString_obj)

Arguments

XNAString_obj

XNAString object

Value

XNAStringSet object

setClassUnion definitions

Description

setClassUnion definitions used in XNAString class. charOrDNAOrRNA consists of character, DNAString, RNAString, DNAStringSet, RNAStringSet. charOrDNA consists of character, DNAString, DNAStringSet

Function which checks if XNAString object satisfies predefined slots length

Description

Function which checks if XNAString object satisfies predefined slots length

Usage

xnastringElementsNumber(
  xnastring_obj,
  cond_name = "==1",
  cond_base,
  cond_sugar,
  cond_backbone,
  cond_target = ">0",
  cond_conj5 = "==1",
  cond_conj3 = "==1"
)

Arguments

xnastring_obj

XNAString object
cond_name

allowed name elements in object
cond_base

allowed base elements in object
cond_sugar

allowed sugar elements in object
cond_backbone

allowed backbone elements in object
cond_target

allowed target elements in object
cond_conj5

allowed conj5 elements in object
cond_conj3

allowed conj3 elements in object

Value

logical

Examples

obj <- XNAString(
  base = c("EAA", "AAA"),
  sugar = c("FFO", "OOO"),
  name = c("a"),
  conjugate5 = c("TTT")
)
xnastringElementsNumber(obj,
  cond_name = "==1",
  cond_base = "%in% c(1,2)",
  cond_sugar = "%in% c(1,2)",
  cond_backbone = "%in% c(1,2)",
  cond_target = ">0",
  cond_conj5 = "==1",
  cond_conj = "==1"
)

Create XNAString object from HELM - user interface

Description

Create XNAString object from HELM - user interface

Usage

XNAStringFromHelm(
  helm,
  name = NA_character_,
  dictionary = xna_dictionary,
  compl_dictionary = complementary_bases,
  remove_linker = TRUE
)

Arguments

helm

string (or strings vector) with HELM sequence, which contains one RNA polymer and optionally CHEM element
name

character (or character vector)
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
remove_linker

logical defines if linker should be clipped from RNA

Value

XNAString object if single helm, XNAStringSet object otherwise

Author(s)

Marianna Plucinska

Examples

XNAStringFromHelm("RNA1{[dR](A)P.[dR](A)P.[dR](A)}$$$$V2.0")
XNAStringFromHelm("RNA1{[dR](A)P.[dR](A)P.[dR](A)}$$$$V2.0", 'name')
XNAStringFromHelm(c("RNA1{[dR](A)P.[dR](A)P.[dR](A)}$$$$V2.0",
                    "RNA1{[dR](T)P.[dR](T)P.[dR](A)}$$$$V2.0"),
                  c('name1', 'name2'))

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))

XNAStringToHelmFun function takes XNAString object and translates base, sugar and backbone to HELM notation

Description

XNAStringToHelmFun function takes XNAString object and translates base, sugar and backbone to HELM notation

Usage

XNAStringToHelm(xnastring_obj, dictionary = xna_dictionary)

Arguments

xnastring_obj

XNAString object
dictionary

HELM-symbol dictionary

Value

string (HELM notation)

Examples

obj <- XNAString(
  base = "AAA",
  sugar = "DDD",
  backbone = "OO"
)
XNAStringToHelm(obj)

This is function finding all the occurrences of a given pattern (typically short) in a (typically long) set of reference sequences.

Description

This is function finding all the occurrences of a given pattern (typically short) in a (typically long) set of reference sequences.

Implementation of this method is based on vmatchPatterrm method from BSgenome

Usage

XNAVmatchPattern(
  pattern,
  subject,
  target.number = 1,
  max.mismatch = 0,
  min.mismatch = 0,
  with.indels = FALSE,
  fixed = TRUE,
  algorithm = "auto",
  exclude = "",
  maskList = logical(0),
  userMask = IRanges::IRangesList(),
  invertUserMask = FALSE
)

## S4 method for signature 'XNAString,character'
XNAVmatchPattern(
  pattern,
  subject,
  target.number = 1,
  max.mismatch = 0,
  min.mismatch = 0,
  with.indels = FALSE,
  fixed = TRUE,
  algorithm = "auto"
)

## S4 method for signature 'XNAString,XStringSet'
XNAVmatchPattern(
  pattern,
  subject,
  target.number = 1,
  max.mismatch = 0,
  min.mismatch = 0,
  with.indels = FALSE,
  fixed = TRUE,
  algorithm = "auto"
)

## S4 method for signature 'XNAString,BSgenome'
XNAVmatchPattern(
  pattern,
  subject,
  target.number = 1,
  max.mismatch = 0,
  min.mismatch = 0,
  with.indels = FALSE,
  fixed = TRUE,
  algorithm = "auto",
  exclude = "",
  maskList = logical(0),
  userMask = IRanges::IRangesList(),
  invertUserMask = FALSE
)

Arguments

pattern

XNAString object with non-empty target slot
subject

string, string vector or DNAString / DNAStringSet / chromosome from BSgenome object
target.number

numeric - if target is a multi-element vector, then specify which element in use. 1 is the default
max.mismatch

The maximum number of mismatching letters allowed. If non-zero, an algorithm that supports inexact matching is used.
min.mismatch

The minimum number of mismatching letters allowed. If non-zero, an algorithm that supports inexact matching is used.
with.indels

If TRUE then indels are allowed. In that case, min.mismatch must be 0 and max.mismatch is interpreted as the maximum "edit distance" allowed between the pattern and a match. Note that in order to avoid pollution by redundant matches, only the "best local matches" are returned. Roughly speaking, a "best local match" is a match that is locally both the closest (to the pattern P) and the shortest.
fixed

If TRUE (the default), an IUPAC ambiguity code in the pattern can only match the same code in the subject, and vice versa. If FALSE, an IUPAC ambiguity code in the pattern can match any letter in the subject that is associated with the code, and vice versa.
algorithm

One of the following: "auto", "naive-exact", "naive-inexact", "boyer-moore", "shift-or" or "indels".
exclude

A character vector with strings that will be used to filter out chromosomes whose names match these strings. Needed for BSParams object if subject is a chromosome object from BSgenome
maskList

A named logical vector of maskStates preferred when used with a BSGenome object. When using the bsapply function, the masks will be set to the states in this vector.
userMask

An IntegerRangesList, containing a mask to be applied to each chromosome.
invertUserMask

Whether the userMask should be inverted.

Value

An MIndex object for vmatchPattern.

Examples

s3 <-
XNAString::XNAString(
 base = "GCGGAGAGAGCACAGATACA",
 sugar = "FODDDDDDDDDDDDDDDDDD",
 target = Biostrings::DNAStringSet(
     c("AAAAGCTTTACAAAATCCAAGATC", "GGCGGAGAGAGCACAGATACA")
 )
)
chrom <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38$chr1
result <- XNAString::XNAMatchPattern(s3, chrom)