ProteinSeq: Details, generics, and methods for the 'ProteinSeq' class

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Details, generics, and methods for the ProteinSeq class

Description

The ProteinSeq class is an input for the functions countSeqDiffs and is.ProteinSeq. It consists of a character vector. Each entry in this vector represents the aminoacid (the protein components coded by a gene) sequence, for a given aligned protein sequence. The object must be a character, named vector, with the names typically corresponding to the species (name could be scientific or common name) from which every sequence came. The characters within the vector must correspond to valid aminoacid symbols (i.e. capitalized letters or deletion "_" symbols). Particularly, the following symbols relate to amino acids: "A", "C", "D", "E", "F", "G", "H", "I", "K", "L", "M", "N", "P", "Q", "R", "S", "T", "V", "W", "Y".

Importantly, the symbol "_" means an indel (insertion or deletion), and the symbols "X", "B", "Z", "J" should be considered as ambiguous site readings.

Usage

is.ProteinSeq(x)

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

## S3 method for class 'ProteinSeq'
summary(object, ...)

## S3 method for class 'ProteinSeq'
head(x, n = 20, ...)

## S3 method for class 'ProteinSeq'
tail(x, n = 20, ...)

Arguments

x	an object of the class ProteinSeq
...	arguments to be passed to or from other methods. #' @return Shows the last n elements of a ProteinSeq object.
object	an object of the class ProteinSeq
n	number of aminoacids to be shown

Details

is.ProteinSeq A ProteinSeq must be a list containing multiple vectors made of characters (usually letters that code to Amino Acids, deletions, etc). All of these must have the correct length (i.e. same as all the others) and their relative positions should match (i.e., the object must contain alligned Amino acide sequences).

Value

A logical indicating if object x is of class ProteinSeq

print.ProteinSeq Prints a brief summary of a print.ProteinSeq containing the number of sequences and the length of the alignment. See more details of the format in ??ProteinSeq.

Same as print.ProteinSeq.

Shows the first n elements of a ProteinSeq object.

Author(s)

Daniel Rabosky, Matheus Januario, Jennifer Auler

evolved documentation built on April 3, 2025, 9:23 p.m.