fetchSequence {dagLogo} | R Documentation |
dagPeptides-class
object.This function fetches protein/peptide sequences from a Biomart database or
from a Proteome-class
object based on protein/peptide IDs and create
a dagPeptides-class
object following restriction as specified by
parameters: anchorAA or anchorPos, upstreamOffset and downstreamOffset.
fetchSequence( IDs, type = "entrezgene", anchorAA = NULL, anchorPos, mart, proteome, upstreamOffset, downstreamOffset )
IDs |
A character vector containing protein/peptide IDs used to fetch
sequences from a Biomart database or a |
type |
A character vector of length 1. The available options are
"entrezgene" and "uniprotswissprot" if parameter |
anchorAA |
A character vector of length 1 or the same length as that of anchorPos, each element of which is a single letter symbol of amino acids, for example, "K" for lysine. |
anchorPos |
A character or numeric vector. Each element of which is (1) a single-letter symbol of amino acid followed by the position of the anchoring amino acid in the target peptide/protein sequence, for example, "K123" for lysine at position 123 or the position of the anchoring amino acid in the target peptide/protein sequence, for example, "123" for an amino acid at position 123; or (2) a vector of subsequences containing the anchoring AAs. |
mart |
A Biomart database name you want to connect to. Either of parameters
|
proteome |
An object of |
upstreamOffset |
An integer, the upstream offset relative to the anchoring position. |
downstreamOffset |
An integer, the downstream offset relative to the anchoring position. |
An object of class dagPeptides-class
## Case 1: You have both positions of the anchoring AAs and the identifiers ## of their enclosing peptide/protein sequences for fetching sequences using ## the fetchSequence function via the Biomart. if (interactive()) { try({ mart <- useMart("ensembl") fly_mart <- useDataset(mart = mart, dataset = "dmelanogaster_gene_ensembl") dat <- read.csv(system.file("extdata", "dagLogoTestData.csv", package = "dagLogo")) seq <- fetchSequence( IDs = as.character(dat$entrez_geneid), anchorPos = as.character(dat$NCBI_site), mart = fly_mart, upstreamOffset = 7, downstreamOffset = 7) head(seq@peptides) }) } ## Case 2: You don't have the exactly postion information, but You have the ## interesting peptide subsequences and the identifiers of their enclosing ## peptide/protein sequences for fetching sequences using the fetchSequence ## function via the Biomart. In the following examples, the anchoring AAs ## are marked by asterisks. if (interactive()) { try({ mart <- useMart("ensembl") fly_mart <- useDataset(mart = mart, dataset = "dmelanogaster_gene_ensembl") dat <- read.csv(system.file("extdata", "dagLogoTestData.csv", package = "dagLogo")) seq <- fetchSequence( IDs = as.character(dat$entrez_geneid), anchorAA = "*", anchorPos = as.character(dat$peptide), mart = fly_mart, upstreamOffset = 7, downstreamOffset = 7 ) head(seq@peptides) }) } ## In following example, the anchoring AAs are lower-case "s" for amino acid ## serine. if(interactive()) { try({ dat <- read.csv(system.file("extdata", "peptides4dagLogo.csv", package = "dagLogo")) mart <- useMart("ensembl") human_mart <- useDataset(mart = mart, dataset = "hsapiens_gene_ensembl") seq <- fetchSequence(IDs = toupper(as.character(dat$symbol)), type = "hgnc_symbol", anchorAA = "s", anchorPos = as.character(dat$peptides), mart = human_mart, upstreamOffset = 7, downstreamOffset = 7) head(seq@peptides) }) }