formatSequence: Format already aligned peptide sequences.

In jianhong/dagLogo: dagLogo: a Bioconductor package for visualizing conserved amino acid sequence pattern in groups based on probability theory

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)

jianhong/dagLogo documentation built on Nov. 5, 2024, 7:46 a.m.