ProteinSeq {evolved} | R Documentation |
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 |
... |
arguments to be passed to or from other methods. #' @return Shows the last |
object |
an object of the class |
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