annotate {cellHTS2} | R Documentation |
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.
## 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). |
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 huber@ebi.ac.uk, Ligia Bras ligia@ebi.ac.uk
Boutros, M., Bras, L.P. and Huber, W. (2006) Analysis of cell-based RNAi screens, Genome Biology 7, R66.
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)