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R: Build a cellHTS2 object from a data frame containing...

buildCellHTS2

R Documentation

Build a cellHTS2 object from a data frame containing measurements

Description

Builds a cellHTS2 object from a data frame.

Usage

buildCellHTS2(xd, measurementNames)

Arguments

`xd`	a data frame containing the columns `plate`, `replicate` and `well`, and the measurement columns. The `plate` and `replicate` columns must contain integer values, starting from 1. The `well` column must contain well names formed by one to two capitals letter followed by two digits, e.g. `A12` or `AB01`. Letter ordering is as follows: A, B, C,..., Z, AA, AB, AC,..., AZ, BA, BB, ..., ZZ.
`measurementNames`	an optional character vector containing the measurement names. If missing, the names of the measurement columns in `xd` are used. If `NULL`, the measurements are not named.

Details

The function uses readPlateList to build a cellHTS2 object.

Value

An object of class cellHTS, which extends the class NChannelSet.

Author(s)

Gregoire Pau gregoire.pau@embl.de

References

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

Examples

wells = sprintf("%s%02d", rep(LETTERS[1:8], each=12), 1:12)
xd = expand.grid(plate=1:3, replicate=1:2, well=wells)
xd$cell.number = rnorm(nrow(xd))
xd$cell.size = rnorm(nrow(xd))
x = buildCellHTS2(xd)

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)

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Type 'license()' or 'licence()' for distribution details.

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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/buildCellHTS2.Rd_%03d_medium.png", width=480, height=480)
> ### Name: buildCellHTS2
> ### Title: Build a cellHTS2 object from a data frame containing
> ###   measurements
> ### Aliases: buildCellHTS2
> 
> ### ** Examples
> 
> wells = sprintf("%s%02d", rep(LETTERS[1:8], each=12), 1:12)
> xd = expand.grid(plate=1:3, replicate=1:2, well=wells)
> xd$cell.number = rnorm(nrow(xd))
> xd$cell.size = rnorm(nrow(xd))
> x = buildCellHTS2(xd)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>