alphabetFrequency {XNAString}R Documentation

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")

[Package XNAString version 1.2.2 Index]