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 |
upstreamOffset |
an integer, upstream offset position |
downstreamOffset |
an integer, downstream offset position |
return an object of dagPeptides
Jianhong Ou, Alexey Stukalov, Julie Zhu
1 2 3 4 5 6 7 | 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)
|
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