formatSequence {dagLogo} | R Documentation

## Format already aligned peptide sequences.

### Description

Convert already aligned peptide sequences into an object of `dagPeptides-class`.

### Usage

    formatSequence(seq, proteome, upstreamOffset, downstreamOffset)

### Arguments

`seq` | A vector of aligned peptide sequences of the same length
`proteome` | An object of `Proteome-class`.
`upstreamOffset` | An integer, the upstream offset relative to the anchoring position.
`downstreamOffset` | An integer, the downstream offset relative to the anchoring position.

### Value

An object of `dagPeptides-class` Class

### Author(s)

Jianhong Ou, Haibo Liu

### Examples

    ## Suppose you already have the aligned peptides sequences at hands. Then you can use
    ## the formatSequence function to prepare an object of dagPeptides. Befor doing
    ## that, you need prepare a Proteome object by the prepareProteome function.

    dat <- unlist(read.delim(system.file(
                                       "extdata", "grB.txt", package = "dagLogo"),
                             header = FALSE, as.is = TRUE))

    ## prepare an object of Proteome Class from a fasta file
    proteome <- prepareProteome(fasta = system.file("extdata",
                                                    "HUMAN.fasta",
                                                    package = "dagLogo"),
                                species = "Homo sapiens")

    ## prepare an object of dagPeptides Class from a Proteome object
    seq <- formatSequence(seq = dat, proteome = proteome, upstreamOffset = 14,
                         downstreamOffset = 15)

[Package dagLogo version 1.25.0 Index]