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

In Modstrings: Working with modified nucleotide 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 = ""))
hasOnlyBaseLetters(mod)
alphabetFrequency(mod)

Example output

Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

There were 50 or more warnings (use warnings() to see the first 50)
[1] FALSE
A C G T N - + . p δ O ] D J e g ` b U ∝ π I 7 6 3 2 1 8 ∉ ⊆ ⊇ R α m h × f 4 ν X 
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 
' κ o ( ) η a ⇓ ⇑ " √ / ≡ ζ ~ 
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 

Modstrings documentation built on Nov. 8, 2020, 7:51 p.m.