annotation: Create trait.annotation object
In byandell/qtlview: Visualization of QTL Scans for Multiple Traits

Description Usage Arguments Details Value Author(s) Examples

Creates a trait.annotation object that associates a_gene_id with Symbol.

1	read.annotation(filename, update.names = NULL, drop.extra = TRUE, ...)

`filename`	File name where gene annotations are found.
`update.names`	Named character vector to translate names in file to `trait.annotation` column names if not `NULL`. See details.
`drop.extra`	Drop extra names in file if `TRUE`.
`...`	~~Describe `...` here~~

The file is read and any name changes are performed. The names of update.names must correspond (partial match) to columns in the returned object. The values of update.names are the (partial) match to column names in the file identified by filename.

The Chromosome_Position column, if missing, is created by averaging theStart Coordinate and End Coordinate columns and rescaling from base pairs to Mb.

A data frame with entries:

`a_substance_id`	Substance ID number.
`accession_code`	Accession code.
`a_gene_id`	Gene ID number.
`Symbol`	Gene symbol.
`Alternate_Symbols`	Alternate gene symbols.
`Name`	Gene name.
`Alternate_Names`	Alternate gene names, comma separated.
`Description`	Gene description.
`Chromosome`	Chromosome name.
`Strand`	Strand direction (+1 or 1).
`Chromosome_Position`	Chromosome position in Mb.

Brian S. Yandell (byandell@wisc.edu)

## Not run: 
## Do this once when creating your cross library.
my.file.name <- "~/Rlib/eqtl/data/Rosetta/F2.Annotation.mm8.20080208.csv"
my.data.lib <- "~/Rlib/eqtl/B6BTBR07"

trait.annotation <- read.annotation(my.file.name,
  update.names = c(Symbol = "gene1", Alternate_Symbols = "gene",
    Name = "Gene_Name", Alternate_Names = "AlternateNames",
    Description = "ProteomeShortDescription",
    Chromosome = "CHROMOSOME", Start_Coordinate = "STARTCOORD",
    End_Coordinate = "ENDCOORD", Strand = "STRAND"))

save("trait.annotation",
  file = file.path(my.data.lib, "data", "trait.annotation.RData"),
  compress = TRUE)

## End(Not run)