cellHTS (version 1.42.0)

annotate: Annotates the gene IDs of a given cellHTS object

Description

Annotate the gene IDs of a given cellHTS object.

Usage

annotate(x, ...)
"annotate"(x, geneIDFile, path, ...)

Arguments

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.

Value

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.

Details

• geneIDFileThis 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

..

See Also

readPlateData, configure

Examples

## 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)