letterFrequency: Calculate the frequency of letters in nucleotide sequence...

In FelixErnst/Modstrings: Working with modified nucleotide sequences

Calculate the frequency of letters in nucleotide sequence with modifications, or the consensus matrix of a set of sequences

Description

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.

Usage

## 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)

Arguments

x	a ModString, a ModStringSet, a ModStringViews or a MaskedModString object.
as.prob	TRUE or FALSE (default): Should the result be returned as probabilities instead of counts? (sum per column = 1)
baseOnly	TRUE or FALSE (default): Should the result omit occurances of the letters N.-+?
collapse	TRUE or FALSE (default): Should the results summed up all elements for ModStringSet or ModStringViews objects or reported per element.
...	See letterFrequency.
letters	See letterFrequency.
OR	See letterFrequency.
shift	See letterFrequency.
width	See letterFrequency.
threshold	Since the amiguityMap is fixed to "?" for ModString objects, only the treshold can be set (default threshold = 0.25)

Value

a matrix with the results (letter x pos).

Examples

mod <- ModDNAString(paste(alphabet(ModDNAString()), collapse = ""))
mod
hasOnlyBaseLetters(mod)
alphabetFrequency(mod)

FelixErnst/Modstrings documentation built on April 1, 2024, 2:21 p.m.