annotate {cellHTS2} | R Documentation

## Annotates the reagents (probes) of a cellHTS object

### Description

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.

### Usage

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

### Arguments

`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).

### Details

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.

### Value

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`.

### Author(s)

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

### References

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

### See Also

`readPlateList`, `configure`

### Examples

        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)

[Package cellHTS2 version 2.8.3 Index]