annotate {cellHTS} | R Documentation |
Annotate the gene IDs of a given cellHTS
object.
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. |
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
..
## 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)