dinucleotideFrequency {XNAString}R Documentation

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
)

[Package XNAString version 1.1.2 Index]