dagLogo (version 1.10.2)

formatSequence: 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

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)
}