dagPeptides-class {dagLogo} | R Documentation

## 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 column 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

[Package dagLogo version 1.30.0 Index]