beadAnalysis {BeadExplorer}R Documentation

Automated Bead Analysis

Description

A function to easily automate standard qc and normalisation analyses of BeadStudio output data

Usage

beadAnalysis(datafile = NULL, qcdatafile = NULL, version, qc = "ArrayQuality.txt", output = "png", normalise = "Quantile", 
bkd="Offset", offset=NULL, outputhtml = TRUE, open = TRUE, manifest="", outputsamples = TRUE, 
outputarrays = TRUE, outputresults = TRUE, return = "Normalised", widget = TRUE)

Arguments

datafile A character vector of a filepath(s) of Illumina BeadStudio 'gene profile.csv' output files
qcdatafile A character vector of a filepath(s) of Illumina BeadStudio "qcinfo.csv" output files
version A character vector, either "one or "two" indicating the version of BeadStduio used to create the QC data file
qc A character of the path to a log file of previously analysed data, as created by Bead Explorer
output A character specifying output types for graphs. Options are "png", "bmp", "jpeg"
normalise A character specifying a normalisation option. Options are "Quantile", "Qspline", "RobustQuantile"
bkd A character spcificying the background adjustment method. Options are "Offset" or "Base"
offset A numeric specifiying the offset value to add
outputhtml A logical specifying whether a html report should be produced
open A logical specifying whether the html report should be opened
manifest Character specifying the path of the Illumina manifest .csv file to use. Adds annotation information to the output results file
outputsamples A logical specifying whether a sample QC graph should be produced
outputarrays A logical specifying whether an array QC graph should be produced
outputresults A logical specifying whether a normalised results file should be produced
return A character specifying a return option. Options are "Raw", "Normalised", "None"
widget A logical specifying whether a widget should be used for input

Details

This is a wrapper function that automates the analysis of BeadStudio output files. Note that the input data can be created using version one or version two of BeadStudio - this must be specified. See vignette for details of widget. All output files will be placed in the current working directory. By submitting multiple separate files, the data will be combined into one analysis. Use default values to run a human example data set.

Value

The return value is determined by the return argument: 'Normalised' returns a normalised beadData-class object, 'Raw' - an unnormalised beadData-class object, 'None' - NULL

Author(s)

Gareth Elvidge gareth.elvidge@well.ox.ac.uk

See Also

normalise, dotplotArrays, plotSamples, help

Examples

## Not run: 
data<-beadAnalysis()
## End(Not run)

[Package BeadExplorer version 1.2.0 Index]