fetchSequence: fetch sequence by id
In alyst/dagLogo: dagLogo

Description Usage Arguments Value Author(s) See Also Examples

fetch amino acid sequence by given identifiers via biomaRt or proteome prepared by prepareProteome

1 2	fetchSequence(IDs, type="entrezgene", anchorAA=NULL, anchorPos, mart, proteome, upstreamOffset, downstreamOffset)

`IDs`	A vector of Identifiers to retrieve peptides
`type`	type of identifiers
`anchorAA`	a vector of character, anchor Amino Acid
`anchorPos`	a vector of character or numeric, anchor position, for example, K121
`mart`	an object of Mart
`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

Jianhong Ou, Alexey Stukalov, Julie Zhu

formatSequence

    mart <- useMart("ensembl", "dmelanogaster_gene_ensembl")
    dat <- read.csv(system.file("extdata", "dagLogoTestData.csv", package="dagLogo"))
    seq <- fetchSequence(as.character(dat$entrez_geneid[1:5]), 
                anchorPos=as.character(dat$NCBI_site[1:5]), 
                mart=mart, 
                upstreamOffset=7, 
                downstreamOffset=7)