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) }