#' @docType data
#' @title An object of \code{\link{Proteome-class}} representing the
#' \emph{Escherichia coli} proteome.
#' @description A dataset containing the \emph{E. coli} proteome.
#' @format
#' An object of \code{\link{Proteome-class}} for Escherichia coli proteome.
#' The format is: A list with one data frame and an character.
#'
#' *`proteome`: 'data.frame': 13780 obs. of 4 variables
#' *`type`: 'character': "UniProt"
#' *`species`: 'character': "Escherichia coli"
#'
#' The format of proteome is
#' *`ENTREZ_GENE`: a character vector, records entrez gene id
#' *`SEQUENCE`: a character vector, peptide sequences
#' *`ID`: a character vector, Uniprot ID
#' *`LEN`: a character vector, length of peptides
#'
#' @source \url{http://www.uniprot.org/}
#'
#' @details
#' used as an example dataset
#'
#' Annotation data obtained by:
#'
#' library(UniProt.ws)
#'
#' taxId(UniProt.ws) <- 562
#'
#' proteome <- prepareProteome(UniProt.ws, species="Escherichia coli")
#'
#' @examples
#' data(ecoli.proteome)
#' head(ecoli.proteome@proteome)
#' ecoli.proteome@type
#' @keywords datasets
"ecoli.proteome"
#' @docType data
#' @title An object of \code{\link{Proteome-class}} representing the subset of
#' \emph{Drosophila melanogaster} proteome.
#' @description The subset \code{\link{Proteome-class}} of fruit fly.
#' @format An object of \code{\link{Proteome-class}} for fly subset proteome.
#' The format is: A list with one data frame and an character.
#'
#' *`proteome`: 'data.frame': 1406 obs. of 4 variables
#' *`type`: 'character': "UniProt"
#' *`species`: 'character': "Drosophila melanogaster"
#'
#' The format of proteome is
#'
#' *`ENTREZ_GENE`: a character vector, records entrez gene id
#' *`SEQUENCE`: a character vector, peptide sequences
#' *`ID`: a character vector, Uniprot ID
#' *`LEN`: a character vector, length of peptides
#'
#' @source \url{http://www.uniprot.org/}
#'
#' @details
#' used as an example dataset
#'
#' Annotation data obtained by:
#'
#' library(UniProt.ws)
#'
#' taxId(UniProt.ws) <- 7227
#'
#' proteome <- prepareProteome(UniProt.ws)
#'
#' proteome@proteome <- proteome@proteome[sample(1:19902, 1406), ]
#'
#' @examples
#' data(proteome.example)
#' head(proteome.example@proteome)
#' proteome.example@type
#' @keywords datasets
"proteome.example"
#' @docType data
#' @title An object of \code{\link{dagPeptides-class}} representing acetylated lysine-containing peptides.
#' @description A dataset containing the acetylated lysine-containing peptides from \emph{Drosophila melanogaster}.
#' @format
#' An object of \code{\link{dagPeptides-class}} Class
#' The format is: A list.
#'
#' *`data`: 'data.frame': 732 obs. of 7 variables
#' *`peptides`: 'matrix': amnio acid in each position
#' *`upstreamOffset`: an integer, upstream offset position
#' *`downstreamOffset`: an integer, downstream offset position
#' *`type`: "character", type of identifiers
#'
#' The format of data is
#'
#' *`IDs`: a character vector, input identifiers
#' *`anchorAA`: a character vector, anchor amino acid provided in inputs
#' *`anchorPos`: a numeric vector, anchor position in the protein
#' *`peptide`: a character vector, peptide sequences
#' *`anchor`: a character vector, anchor amino acid in the protein
#' *`upstream`: a character vector, upstream peptides
#' *`downstream`: a character vector, downstream peptides
#'
#' @details
#' used as an example dataset
#'
#' seq obtained by:
#'
#' mart <- useMart("ensembl", "dmelanogaster_gene_ensembl")
#'
#' dat <- read.csv(system.file("extdata", "dagLogoTestData.csv", package="dagLogo"))
#'
#' seq <- fetchSequence(as.character(dat$entrez_geneid),
#'
#' anchorPos=as.character(dat$NCBI_site),
#'
#' mart=mart,
#'
#' upstreamOffset=7,
#'
#' downstreamOffset=7)
#' @examples
#' data(seq.example)
#' head(seq.example@peptides)
#' seq.example@upstreamOffset
#' seq.example@downstreamOffset
#' @keywords datasets
#'
"seq.example"
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.