alphabetFrequency {XNAString} | R Documentation |
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.
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 )
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 |
matrix (frequency matrix for a given slot)
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")