R: Annotates the gene IDs of a given cellHTS object
annotate
R Documentation
Annotates the gene IDs of a given cellHTS object
Description
Annotate the gene IDs of a given cellHTS object.
Usage
annotate(x, ...)
## S3 method for class 'cellHTS'
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.
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.
Value
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.