PeptideAtlasBuilder_DB: Build data package for experimentally identified peptides
In PAnnBuilder: Protein annotation data package builder

Description Usage Arguments Details Value Author(s) Examples

This function creates a data package for peptides identified in a large set of tandem mass spectrometry proteomics experiments.

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PeptideAtlasBuilder_DB(name = c("Human","Human Plasma","Saccharomyces cerevisiae",
                    "Drosophila Melanogaster","Mouse Plasma","Halobacterium"),
                    prefix, pkgPath, version, author)

`name`	a character string to indicate which organisms or important sample groups will be built.
`prefix`	the prefix of the name of the data package to be built. (e.g. "hsaSP"). The name of builded package is prefix+".db".
`pkgPath`	a character string for the full path of an existing directory where the built backage will be stored.
`version`	a character string for the version number.
`author`	a list with named elements "authors" containing a character vector of author names and "maintainer" containing the complete character string for the maintainer field, for example, "Jane Doe <jdoe@doe.com>".

Build annotation data packages for peptides identified in a large set of tandem mass spectrometry proteomics experiments. Data are from PeptideAtlas database: http://www.peptideatlas.org, including high quality peptide sequences, their locations relative to the protein start (CDS coordinates), and peptide locations in chromosomal coordinates.

PeptideAtlasBuilder_DB employes functions writePeptideAtlasData_DB to parse and write data.

Data files in the database will be automatically downloaded to the tmp directory, so enough space is needed for the data files. After downloading, files are parsed by perl, so perl must be installed. It may take a long time to parse database and build R package. Alternatively, we have produced diverse R packages by PAnnBuilder, and you can download appropriate package via http://www.biosino.org/PAnnBuilder.

This function does not return any value.

Hong Li

# Set path, version and author for the package.
pkgPath <- tempdir()
version <- "1.0.0"
author <- list()
author[["authors"]] <- "Hong Li"
author[["maintainer"]] <- "Hong Li <sysptm@gmail.com>"

## It may take a long time to parse database and build R package.
# Build annotation data packages "org.Hs.pep.db" for Human PeptideAtlas.
if(interactive()){
    PeptideAtlasBuilder_DB(name = "Human",
                        prefix = "org.Hs.pep", pkgPath, version, author) 
}