AnnotationForge: makeOrgPackage – R documentation

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makeOrgPackage

Making an organism package from annotations available from a set of named data.frames.

Description

The makeOrgPackage function allows the user to make an organism package from any collection of data frames that are united by a common gene ID.

Usage

makeOrgPackage(...,
                 version,
                 maintainer,
                 author,
                 outputDir=getwd(),
                 tax_id,
                 genus=NULL,
                 species=NULL,
                 goTable=NULL,
                 verbose=TRUE)

Arguments

`...`	A set of data.frames containing annotation data. Each of these arguments must be named. Those names will become the names of the tables in the final database. Also, there are no rownames for these data.frames, and the colnames are the names that will be used as extractable fields in the final package. In other words they will be what comes back when you call `columns` and `keytypes` Finally, the 1st column of every data.frame must be labeled GID, and correspond to a gene ID that is universal for the entire set of data.frames. The GID is how the different tables will be joined internally
`version`	What is the version number for this package? format: \'x.y.z\'
`maintainer`	Who is the package maintainer? (must include email to be valid)
`author`	Who is the creator of this package?
`outputDir`	A path where the package source should be assembled.
`tax_id`	The Taxonomy ID that represents your organism. (NCBI has a nice online browser for finding the one you need)
`genus`	Single string indicating the genus.
`species`	Single string indicating the species.
`goTable`	By default, this is NULL, but if one of your '...' data.frames has GO annotations, then this name will be the name of that argument. When you specify this, `makeOrgPackage` will process that data.frame to remove extra GO terms (that are too new for the current GO.db) and also will generate a table for GOALL data (based on ancestor terms for each mapping from GO.db) and for each ontology. This table will also be checked to make sure that it has exactly THREE columns, that must be named GID, GO and EVIDENCE. These must correspond to the gene IDs, GO IDs and evidence codes respectively. GO IDs should be formatted like this to work with other DBs in the project: \'GO:XXXXXXX\'.
`verbose`	When TRUE progress messages are displayed.

Value

The path to the package that just created. This is useful for calling install.packages as the next step.

Author(s)

M. Carlson

Examples

if(interactive()){

## Makes an organism package for Zebra Finch data.frames:
finchFile <- system.file("extdata","finch_info.txt",package="AnnotationForge")
finch <- read.table(finchFile,sep="\t")

## not that this is how it should always be, but that it *could* be this way.
fSym <- finch[,c(2,3,9)]
fSym <- fSym[fSym[,2]!="-",]
fSym <- fSym[fSym[,3]!="-",]
colnames(fSym) <- c("GID","SYMBOL","GENENAME")

fChr <- finch[,c(2,7)]
fChr <- fChr[fChr[,2]!="-",]
colnames(fChr) <- c("GID","CHROMOSOME")

finchGOFile <- system.file("extdata","GO_finch.txt",package="AnnotationForge")
fGO <- read.table(finchGOFile,sep="\t")
fGO <- fGO[fGO[,2]!="",]
fGO <- fGO[fGO[,3]!="",]
colnames(fGO) <- c("GID","GO","EVIDENCE")

makeOrgPackage(gene_info=fSym, chromosome=fChr, go=fGO,
               version="0.1",
               maintainer="Some One <so@someplace.org>",
               author="Some One <so@someplace.org>",
               outputDir = ".",
               tax_id="59729",
               genus="Taeniopygia",
               species="guttata",
               goTable="go")

## then you can call install.packages based on the return value
install.packages("./org.Tguttata.eg.db", repos=NULL)

}

AnnotationForge

Tools for building SQLite-based annotation data packages

v1.32.0

Artistic-2.0

Authors

Marc Carlson, Hervé Pagès

Initial release