qcBeadLevel {beadarray}R Documentation

Generate simple diagnostic plots for Illumina bead level data

Description

Generate simple diagnostic plots for Illumina bead level data

Usage

qcBeadLevel(object, whatToPlot="G", RG=FALSE, log=TRUE, nrow = 100, ncol= 100,
                    colDens=1, colBox=0, html=TRUE,
                    fileName="qcsummary.htm", plotdir=NULL,
                    experimentName=NULL, targets=NULL, ...)

Arguments

object a BeadLevelList object
whatToPlot character string or vector specifying which intensities to plot. Possibilities are "G", "Gb" for single channel data and "G", "Gb", "R" and "Rb" for two-colour data
RG if TRUE, plot R vs G intensities per array. Default value is FALSE. Only useful for two-channel data
log if TRUE log2 intensities are plotted
nrow How many rows should the array be divided into (used by imageplot)
ncol How many columns should the array be divided into (used by imageplot)
colDens colors for density plots (default is 1)
colBox colors for box plot (default is 0)
html logical scalar. If TRUE an html summary page is generated. If FALSE, no summary page is generated.
fileName name of html summary page. Default is 'qcsummary.htm'.
plotdir optional character string specifying the filepath where the plots will be saved. Defaults to current working directory.
experimentName name to appear on HTML report (default is NULL).
targets data.frame containing smaple information
... further arguments that can be passed to the plotting functions.

Details

This function creates boxplots, smoothed histogram (density) plots and imageplots of raw bead level intensity data.

An html page which displays the results, is created when html=TRUE. The html page name is specified by the fileName argument.

Author(s)

Matt Ritchie

Examples

#data(BLData)
#qcBeadLevel(BLData)

[Package beadarray version 1.6.0 Index]