letterFrequency {Modstrings} | R Documentation |
These functions follow the same principle as the
Biostrings
functions. Please be
aware, that the matices can become quite large, since the alphabet of
ModString
objects contains more letters.
## S4 method for signature 'ModDNAString' hasOnlyBaseLetters(x) ## S4 method for signature 'ModRNAString' hasOnlyBaseLetters(x) ## S4 method for signature 'ModDNAString' alphabetFrequency(x, as.prob = FALSE, baseOnly = FALSE) ## S4 method for signature 'ModRNAString' alphabetFrequency(x, as.prob = FALSE, baseOnly = FALSE) ## S4 method for signature 'ModDNAStringSet' alphabetFrequency(x, as.prob = FALSE, collapse = FALSE, baseOnly = FALSE) ## S4 method for signature 'ModRNAStringSet' alphabetFrequency(x, as.prob = FALSE, collapse = FALSE, baseOnly = FALSE) ## S4 method for signature 'MaskedModString' alphabetFrequency(x, as.prob = FALSE, ...) ## S4 method for signature 'ModStringViews' letterFrequency(x, letters, OR = "|", as.prob = FALSE, ...) ## S4 method for signature 'MaskedModString' letterFrequency(x, letters, OR = "|", as.prob = FALSE) ## S4 method for signature 'ModStringSet' consensusMatrix(x, as.prob = FALSE, shift = 0L, width = NULL, baseOnly = FALSE) ## S4 method for signature 'ModDNAStringSet' consensusString(x, threshold = 0.25, shift = 0L, width = NULL) ## S4 method for signature 'ModRNAStringSet' consensusString(x, threshold = 0.25, shift = 0L, width = NULL) ## S4 method for signature 'ModStringViews' consensusString(x, threshold, shift = 0L, width = NULL)
x |
a |
as.prob |
|
baseOnly |
|
collapse |
|
... |
See |
letters |
See |
OR |
See |
shift |
See |
width |
See |
threshold |
Since the amiguityMap is fixed to |
a matrix with the results (letter x pos).
mod <- ModDNAString(paste(alphabet(ModDNAString()), collapse = "")) hasOnlyBaseLetters(mod) alphabetFrequency(mod)