annotate {cellHTS2} | R Documentation |
Annotate the gene IDs of a given cellHTS
object.
## 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 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 . |
Plate
, Well
and GeneID
. The contents of Plate
are expected to be integer. Further columns are allowed.
An S4 object of class cellHTS
,
which inherits from class NChannelSet
.
The following slots are updates after calling this function:
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)