fetch sequence by id

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Description

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

Usage

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

Arguments

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. Or a vector of character with amino acid sequences. If AA sequences is used, the anchorAA must be the a vector of character with single AA for each.

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

Value

return an object of dagPeptides

Author(s)

Jianhong Ou, Alexey Stukalov, Julie Zhu

See Also

formatSequence

Examples

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if(interactive()){
    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)
    ## sample: use sequence as anchorPos
    sequences <- seq@peptides
    sequences[, 8] <- "k"
    sequences <- apply(sequences, 1, paste, collapse="")
    seq <- fetchSequence(as.character(seq@data$IDs),
                        anchorAA="k",
                        anchorPos=sequences,
                        mart=mart,
                        upstreamOffset=7,
                        downstreamOffset=7)
    ## sample: use sequence as anchorPos 2
    sequences <- cbind(seq@peptides[, 1:8], "*", seq@peptides[, 9:15])
    sequences <- apply(sequences, 1, paste, collapse="")
    seq <- fetchSequence(as.character(seq@data$IDs),
                        anchorAA="*",
                        anchorPos=sequences,
                        mart=mart,
                        upstreamOffset=7,
                        downstreamOffset=7)
}