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Last data update: 2014.03.03

R: Annotates the reagents (probes) of a cellHTS object

annotate

R Documentation

Annotates the reagents (probes) of a cellHTS object

Description

Annotate the reagents (probes) of a cellHTS object. In RNAi-screens, there is a often a 1:1 correspondence between reagents and intended target genes, hence in this software package the term gene ID is used as a synonym.

Usage

## S4 method for signature 'cellHTS'
annotate(object, geneIDFile, path)

Arguments

`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 in each plate.
`path`	a character of length 1 indicating the path in which to find the gene annotation file (optional).

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 S4 object of class cellHTS, which is obtained by copying object and updating the following slots:

`featureData`	the contents of the annotation file are stored here.
`state`	the processing status of the `cellHTS` object is updated to `state["annotated"]= TRUE`.

Author(s)

Wolfgang Huber, Ligia Bras

References

Boutros, M., Bras, L.P. and Huber, W. (2006) Analysis of cell-based RNAi screens, Genome Biology 7, R66.

Examples


    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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(cellHTS2)
Loading required package: RColorBrewer
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: genefilter
Loading required package: splots
Loading required package: vsn
Loading required package: hwriter
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/cellHTS2/annotate.Rd_%03d_medium.png", width=480, height=480)
> ### Name: annotate
> ### Title: Annotates the reagents (probes) of a cellHTS object
> ### Aliases: annotate annotate,cellHTS-method
> 
> ### ** Examples
> 
> 
>     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)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>