formatSequence: prepare an object of dagPeptides from sequences
In alyst/dagLogo: dagLogo

Description Usage Arguments Value Author(s) See Also Examples

prepare an object of dagPeptides from sequences

1	formatSequence(seq, proteome, upstreamOffset, downstreamOffset)

`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

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

Jianhong Ou, Julie Zhu

fetchSequence

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)
}