validate_seq

Validate character strings before sequence construction.

internal

Classes and functions to work with biological sequences (DNA, RNA and amino acid sequences).
Implements S3 infrastructure to work with biological sequences as described in Keck (2020) <doi:10.1111/2041-210X.13490>.
Provides a collection of functions to perform biological conversion among classes
(transcription, translation) and basic operations on sequences
(detection, selection and replacement based on positions or patterns).
The package also provides functions to import and export sequences from and to other package formats.

Francois Keck

bioseq

A Toolbox for Manipulating Biological Sequences

validate_seq function

<dl><dt>x</dt>
<dd>a character vector.</dd>
<dt>alphabet</dt>
<dd>a character vector defining the sequence alphabet;</dd>
<dt>invalid_replacement</dt>
<dd>a character to replace non valid characters</dd>
<dt>type</dt>
<dd>type of sequence ("DNA", "RNA", "AA"). It is only
used to provide more informative warning messages.</dd></dl>

Arguments

Sequence validator — validate_seq

<dl>

<dt>x</dt>
<dd>a character vector.</dd>


<dt>alphabet</dt>
<dd>a character vector defining the sequence alphabet;</dd>


<dt>invalid_replacement</dt>
<dd>a character to replace non valid characters</dd>


<dt>type</dt>
<dd>type of sequence ("DNA", "RNA", "AA"). It is only
used to provide more informative warning messages.</dd>

</dl>

validate_seq: Sequence validator

Description

Usage

Value

Arguments

Details