fetchSequence {dagLogo} | R Documentation

## Fetch protein/peptide sequences and create a `dagPeptides-class` object.

### Description

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.

### Usage

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

### Arguments

`IDs` | A character vector containing protein/peptide IDs used to fetch sequences from a Biomart database or a `Proteome-class` object.
`type` | A character vector of length 1. The available options are "entrezgene" and "uniprotswissprot" if parameter `mart` is missing; otherwise it can be any type of IDs available in Biomart databases.
`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 `mart` or `proteome` should be provided.
`proteome` | An object of `Proteome-class`. Either of parameters `mart` or `Proteome-class` should be provided.
`upstreamOffset` | An integer, the upstream offset relative to the anchoring position.
`downstreamOffset` | An integer, the downstream offset relative to the anchoring position.

### Value

An object of class `dagPeptides-class`

### Examples

    ## 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)
        })
    }

[Package dagLogo version 1.25.0 Index]