annotate: Annotates the reagents (probes) of a cellHTS object
In cellHTS2: Analysis of cell-based screens - revised version of cellHTS

Description Usage Arguments Details Value Author(s) References See Also Examples

Annotate the reagents (probes) of a cellHTS object. In RNAi-screens, there is a often a 1:1 correspondence between reagents and intended target genes, hence in this software package the term gene ID is used as a synonym.

1 2	## S4 method for signature 'cellHTS' annotate(object, geneIDFile, path)

`object`	a `cellHTS` object.
`geneIDFile`	the name of the file with the gene IDs (see details). This argument is just passed on to the `read.table` function, so any of the valid argument types for `read.table` are valid here, too. Must contain one row for each well in each plate.
`path`	a character of length 1 indicating the path in which to find the gene annotation file (optional).

geneIDFile: This file is expected to be a tab-delimited file with at least three columns, and column names Plate, Well and GeneID. The contents of Plate are expected to be integer. Further columns are allowed.

An S4 object of class cellHTS, which is obtained by copying object and updating the following slots:

`featureData`	the contents of the annotation file are stored here.
`state`	the processing status of the `cellHTS` object is updated to `state["annotated"]= TRUE`.

Wolfgang Huber, Ligia Bras

Boutros, M., Bras, L.P. and Huber, W. (2006) Analysis of cell-based RNAi screens, Genome Biology 7, R66.

readPlateList, configure

    datadir <- system.file("KcViabSmall", package = "cellHTS2")
    x <- readPlateList("Platelist.txt", path=datadir, name="KcViabSmall")
    x <- configure(x, "Description.txt", "Plateconf.txt", "Screenlog.txt", path=datadir)
    x <- annotate(x, "GeneIDs_Dm_HFAsubset_1.1.txt", path=datadir)