Computing the dynamic range

Description

Computes the dynamic range per plate for a complete dataset file and plots the results.

Usage

DRQualControl(header, data, nbLinesHeader, channel, plotTitle, showPlot)

Arguments

Value

Returns the dynamic range for each plate in the shell and saves them in a text file. The name of the text file will be the concatenation of the experiment name specified in the header and the character string "DR.txt".

Shows a plot of the dynamic range values and saves it as a pdf file under the experiment name specified in the header concatenated with the function argument plotTitle.

References

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

Examples

data(exampleHeader, package="RNAither")
data(exampleDataset, package="RNAither")

DRQualControl(header, dataset, 3, "SigIntensity", "DR per plate", 1)

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 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> library(RNAither)
Loading required package: topGO
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

Loading required package: graph
Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums


Loading required package: SparseM

Attaching package: 'SparseM'

The following object is masked from 'package:base':

    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: 'topGO'

The following object is masked from 'package:IRanges':

    members

Loading required package: RankProd
Loading required package: prada
Loading required package: RColorBrewer
Loading required package: grid

Attaching package: 'grid'

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    depth

Loading required package: rrcov
Loading required package: robustbase

Attaching package: 'robustbase'

The following object is masked from 'package:Biobase':

    rowMedians

Scalable Robust Estimators with High Breakdown Point (version 1.3-11)


Attaching package: 'RNAither'

The following object is masked from 'package:IRanges':

    trim

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RNAither/DRQualControl.Rd_%03d_medium.png", width=480, height=480)
> ### Name: DRQualControl
> ### Title: Computing the dynamic range
> ### Aliases: DRQualControl
> ### Keywords: device
> 
> ### ** Examples
> 
> data(exampleHeader, package="RNAither")
> data(exampleDataset, package="RNAither")
> 
> DRQualControl(header, dataset, 3, "SigIntensity", "DR per plate", 1)
[1] 
[1] The dynamic range for Experiment 1 Plate 1 is 2.26260144375196
[1] The dynamic range for Experiment 1 Plate 2 is 1.4881155677732
[1] The dynamic range for Experiment 2 Plate 1 is 2.60163635905914
[1] The dynamic range for Experiment 2 Plate 2 is 1.73348253163042
[1] 
png 
  2 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>