annotate {cellHTS} | 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

geneIDFile
  This 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`.

### Author(s)

Wolfgang Huber huber@ebi.ac.uk, Ligia Braz ligia@ebi.ac.uk

### 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)

[Package cellHTS version 1.10.0 Index]