formatSequence {dagLogo} | R Documentation

## prepare an object of dagPeptides from sequences

### Description

prepare an object of dagPeptides from sequences

### Usage

    formatSequence(seq, proteome, upstreamOffset, downstreamOffset)

### Arguments

`seq` | a vector of character, amino acid sequences
`proteome` | an object of Proteome, output of `prepareProteome`
`upstreamOffset` | an integer, upstream offset position
`downstreamOffset` | an integer, downstream offset position

### Value

return an object of dagPeptides, which is a list contains: data, peptides, upstreamOffset, downstreamOffset and type information

### Author(s)

Jianhong Ou, Julie Zhu

### See Also

`fetchSequence`

### Examples

    if(interactive()){
        dat <- unlist(read.delim(system.file("extdata",
                                "grB.txt", package="dagLogo"),
                                header=F, as.is=TRUE))
        proteome <- prepareProteome(fasta=system.file("extdata",
                                                  "HUMAN.fasta",
                                                  package="dagLogo"))
        seq <- formatSequence(dat, proteome)
    }

[Package dagLogo version 1.16.1 Index]