| fetchSequence {dagLogo} | R Documentation |
fetch amino acid sequence by given identifiers via biomaRt or proteome prepared by prepareProteome
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. 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 |
upstreamOffset |
an integer, upstream offset position |
downstreamOffset |
an integer, downstream offset position |
return an object of dagPeptides
Jianhong Ou, Alexey Stukalov, Julie Zhu
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)
}