plotRG {beadarray}R Documentation

Plot bead level data: R vs G intensities

Description

Shows R and G intensities fom a BeadLevelList object. The beads can either be defined to be all beads with particular ProbeIDs or rows BeadIDs

Usage

plotRG(BLData, ProbeIDs=NULL, BeadIDs=NULL, log=TRUE, arrays=1,
                   xlim=c(8,16), ylim=c(8,16), xlab="G intensities",
                   ylab="R intensities",
                   main=arrayNames(BLData)[arrays], smooth=TRUE,
                   cols=NULL, ...)

Arguments

BLData a BeadLevelList object
ProbeIDs a vector of ProbeIDs to plot
BeadIDs logical/integer vector specifying which rows of data to plot (used if ProbeIDs is NULL)
log logical, if TRUE, take log base 2 of intensities
arrays which array/s to plot
xlim x-axis limits for plot
ylim y-axis limits for plot
xlab character string specifying x-axis label
ylab character string specifying y-axis label
main main plot title
smooth logical, whether to smooth the points (only used when one array is selected for plotting)
cols colours to use on the plot
... further graphical parameters to plot

Details

The R and G intensities from selected beads and arrays are plotted.

Value

Plot is produced on the current graphical device.

Author(s)

Matt Ritchie

Examples

data(BLData)

#plot all beads from array 1
plotRG(BLData, arrays=1)

#plot Beads with ProbeIDs 2 on arrays 1-4
plotRG(BLData, arrays=1:4, ProbeIDs=1000, pch=16)

[Package beadarray version 1.4.0 Index]