annotate: Annotates the gene IDs of a given cellHTS object
In cellHTS: Analysis of cell-based screens

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

Annotate the gene IDs of a given cellHTS object.

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annotate(x, ...)
## S3 method for class 'cellHTS'
annotate(x, geneIDFile, path, ...)

`x`	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 and each plate.
`path`	a character of length 1 indicating the path in which to find the gene annotation file. By default, it can extract the path from `geneIDFile`.
`...`	additional parameters - ignored.

geneIDFileThis 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 S3 object of class cellHTS, which extends the argument x by the following element:

geneAnno

a data.frame containing what was read from input file geneIDFile. The number of rows is equal to the product between the number of wells in each plate and the number of plates.

Moreover, the processing status of the cellHTS object is updated in the slot state to x$state["annotated"]= TRUE. There are methods print.cellHTS, configure.cellHTS and annotate.cellHTS.

Wolfgang Huber huber@ebi.ac.uk, Ligia Braz ligia@ebi.ac.uk

readPlateData, configure

## Not run: 
    datadir <- system.file("KcViabSmall", package = "cellHTS")
    x <- readPlateData("Platelist.txt", "KcViabSmall", path=datadir)
    x <- configure(x, "Plateconf.txt", "Screenlog.txt", "Description.txt", path=datadir)
    x <- annotate(x, "GeneIDs_Dm_HFAsubset_1.1.txt", path=datadir)

## End(Not run)