Class dagPeptides. An S4 class to represent formatted, aligned peptides for dagLogo analysis.

Description

Class dagPeptides. An S4 class to represent formatted, aligned peptides for dagLogo analysis.

Slots

data

A data frame with columns names: IDs, anchorAA, anchorPos, peptide and anchor.

peptides

A matrix of character, each element is a single-character symbol for a amino acid.

upstreamOffset

An integer, the upstream offset relative to the anchoring position.

downstreamOffset

An integer, the downstream offset relative to the anchoring position.

type

A character vector of length 1. Available options :"UniProt", and "fasta" if the dagPeptides object is generated using the function formatSequence, or "entrezgene" and "uniprotswissprot" if generated by the function fetchSequence.

Objects from the Class

Objects can be created by calls of the form

new("dagPeptides", data, peptides, upstreamOffset, downstreamOffset, type).

Author(s)

Jianhong Ou