cellHTS2 (version 2.36.0)

annotate: 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

"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).

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.

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.

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)