tilingArray (version 1.50.0)

qcPlots: Generate simple diagnostic plots for Affymetrix tiling array data

Description

Generate simple diagnostic plots for Affymetrix tiling array data

Usage

qcPlots(x, html=TRUE, plotdir=NULL, probeAnno, gff,  chr=4, coord=c(230000,245000), 		    nr = 2560, nc = 2560,
		    ylimchrom=c(5,16), nucleicAcid, pmindex, pgm=TRUE, ext=".cel", ranks=FALSE, ...)

Arguments

x

ExpressionSet containing the data to be plotted.

html

logical scalar. If TRUE an html summary page 'qcsummary.htm' is generated. If FALSE, no summary page is generated.

plotdir

optional character string specifying the filepath where the plots will be saved. Defaults to current working directory.

probeAnno

environment with probe annotations. See package davidTiling for an example (?probeAnno).

gff

data frame with genome annotation from the GFF file.

chr

integer of length 1 indicating the chromosome number to plot.

coord

integer vector of length 2 containing the start and end coordinates (in bases) for the along chromosome intensity plot.

nr

integer, indicating the number of probes in each row on the array (2560 for yeast tiling arrays).

nc

integer, indicating the number of probes in each column on the array (2560 for yeast tiling arrays).

ylimchrom

numeric vector containing the y limits of the along chromosome intensity plot.

nucleicAcid

character vector or factor indicating what sample has been hybridised to each array. Used to color the boxplots and smoothed histograms of intensities.

pmindex

integer vector of indices of PM probes in x. If missing, this information is extracted from probeAnno.

pgm

logical scalar. If TRUE, image plots will be saved as .pgm files. Otherwise (FALSE), they are converted to jpegs. On windows machines, this argument should be set to TRUE.

ext

character string indicating the file extension.

ranks

logical scalar. If TRUE, imageplots will show ranks of standardised probe intensities. Otherwise (FALSE, default), the standardised probe intensities are plotted.

...

further arguments that can be passed to the plotting function plotSegmentationDots.

Details

This function creates boxplots, smoothed histogram (density) plots, imageplots and along chromosome plots of the raw (log base 2) probe intensity data. An html page called 'qcsummary.htm' which displays the results, is created when html=TRUE.

Imageplots of standardised intensities (i.e. (probe intensity - minimum probe intensity) divided by the difference between the maximum and minimum probe intensities, all on log base 2 scale) or the ranks of these standardised intensities are plotted depending on the ranks argument.

The individual plots are named by replacing the file extension (specified by ext) of each 'celfile.ext', with 'density.png' for smoothed histogram plots, 'gencoord.jpg', for along chromosome plots and either 'log.pgm' ('log.jpg' if pgm=FALSE) or 'rank.pgm' ('rank.jpg' if pgm=FALSE) for the imageplots, depending on the ranks argument.

Examples

## data(davidTiling)
## data(probeAnno)
## qcPlots(davidTiling, probeAnno)