R: Amino Acid Sequences

AAbin {ape} | R Documentation

## Amino Acid Sequences

### Description

These functions help to create and manipulate AA sequences.

### Usage

    ## S3 method for class 'AAbin'
    print(x, ...)

    ## S3 method for class 'AAbin'
    x[i, j, drop = FALSE]

    ## S3 method for class 'AAbin'
    c(..., recursive = FALSE)

    ## S3 method for class 'AAbin'
    rbind(...)
    ## S3 method for class 'AAbin'
    cbind(..., check.names = TRUE, fill.with.Xs = FALSE,
                 quiet = FALSE)

    ## S3 method for class 'AAbin'
    as.character(x, ...)

    ## S3 method for class 'AAbin'
    labels(object, ...)

    ## S3 method for class 'AAbin'
    image(x, what, col, bg = "white", xlab = "", ylab = "",
          show.labels = TRUE, cex.lab = 1, legend = TRUE, grid = FALSE,
          show.aa = FALSE, aa.cex = 1, aa.font = 1, aa.col = "black",...)

    as.AAbin(x, ...)
    ## S3 method for class 'character'
    as.AAbin(x, ...)

    ## S3 method for class 'list'
    as.AAbin(x, ...)

    ## S3 method for class 'AAString'
    as.AAbin(x, ...)

    ## S3 method for class 'AAStringSet'
    as.AAbin(x, ...)

    ## S3 method for class 'AAMultipleAlignment'
    as.AAbin(x, ...)

    ## S3 method for class 'AAbin'
    as.list(x, ...)

    ## S3 method for class 'AAbin'
    as.matrix(x, ...)

    ## S3 method for class 'AAbin'
    as.phyDat(x, ...)

    dist.aa(x, pairwise.deletion = FALSE, scaled = FALSE)
    AAsubst(x)

### Arguments

`x, object` | an object of class `"AAbin"` (or else depending on the function).
`i, j` | indices of the rows and/or columns to select or to drop. They may be numeric, logical, or character (in the same way than for standard R objects).
`drop` | logical; if `TRUE`, the returned object is of the lowest possible dimension.
`recursive` | logical; whether to go down lists and concatenate its elements.
`check.names` | a logical specifying whether to check the rownames before binding the columns (see details).
`fill.with.Xs` | a logical indicating whether to keep all possible individuals as indicating by the rownames, and eventually filling the missing data with insertion gaps (ignored if `check.names = FALSE`).
`quiet` | a logical to switch off warning messages when some rows are dropped.
`what` | a vector of characters specifying the amino acids to visualize. Currently, the only possible choice is to show the three categories hydrophobic, small, and hydrophilic.
`col` | a vector of colours. If missing, this is set to “red”, “yellow” and “blue”.
`bg` | the colour used for AA codes not among `what` (typically X and *).
`xlab` | the label for the x-axis; none by default.
`ylab` | Idem for the y-axis. Note that by default, the labels of the sequences are printed on the y-axis (see next option).
`show.labels` | a logical controlling whether the sequence labels are printed (`TRUE` by default).
`cex.lab` | a single numeric controlling the size of the sequence labels. Use `cex.axis` to control the size of the annotations on the x-axis.
`legend` | a logical controlling whether the legend is plotted (`TRUE` by default).
`grid` | a logical controlling whether to draw a grid (`FALSE` by default).
`show.aa` | a logical controlling whether to show the AA symbols (`FALSE` by default).
`aa.cex, aa.font, aa.col` | control the aspect of the AA symbols (ignored if the previous is `FALSE`).
`pairwise.deletion` | a logical indicating whether to delete the sites with missing data in a pairwise way. The default is to delete the sites with at least one missing data for all sequences.
`scaled` | a logical value specifying whether to scale the number of AA differences by the sequence length.
`...` | further arguments to be passed to or from other methods.

### Details

These functions help to manipulate amino acid sequences of class `"AAbin"`. These objects are stored in vectors, matrices, or lists which can be manipulated with the usual `[` operator.

There is a conversion function to and from characters.

The function `dist.aa` computes the number of AA differences between each pair of sequences in a matrix; this can be scaled by the sequence length. See the function `dist.ml` in phangorn for evolutionary distances with AA sequences.

The function `AAsubst` returns the indices of the polymorphic sites (similar to `seg.sites` for DNA sequences; see examples below).

The two functions `cbind.AAbin` and `rbind.AAbin` work in the same way than the similar methods for the class `"DNAbin"`: see `cbind.DNAbin` for more explanations about their respective behaviours.

### Value

an object of class `"AAbin"`, `"character"`, `"dist"`, or `"numeric"`, depending on the function.

### Author(s)

Emmanuel Paradis, Franz Krah

### See Also

`read.FASTA`, `trans`, `alview`

### Examples

    data(woodmouse)
    AA <- trans(woodmouse, 2)
    seg.sites(woodmouse)
    AAsubst(AA)

[Package ape version 5.4 Index]