formatSequence {dagLogo} | R Documentation |
Convert already aligned peptide sequences into an object of
dagPeptides-class
Class.
formatSequence(seq, proteome, upstreamOffset, downstreamOffset)
seq |
A vector of aligned peptide sequences of the same length |
proteome |
An object of |
upstreamOffset |
An integer, the upstream offset relative to the anchoring position. |
downstreamOffset |
An integer, the downstream offset relative to the anchoring position. |
An object of dagPeptides-class
Class
Jianhong Ou, Haibo Liu
## You already have the aligned peptides sequences in hand. 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 seq <- formatSequence(seq = dat, proteome = proteome, upstreamOffset = 14, downstreamOffset = 15)