qcBeadLevel {beadarray} | R Documentation |
Generate simple diagnostic plots for Illumina bead level data
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, ...)
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. |
This function creates boxplots, smoothed histogram (density) plots and imageplots of raw bead level intensity data.
An html page called 'qcsummary.htm' which displays the results, is created when html=TRUE
.
Matt Ritchie
#data(BLData) #qcBeadLevel(BLData)