MakePDF {aCGH.Spline}R Documentation

Write a PDF containing some normalisation plots.

Description

This function creates a PDF containing various figures to show the quality of normalisation.

Usage

MakePDF(filename, x, raw, ntyp="percentile", p=0.68, fact=4.5, segN=FALSE, sn=0.75)

Arguments

filename - character argument, the output file name.
x - the ".temp" formatted data structure after normalisation.
raw - the".temp" formatted data structure before normalisation.
ntyp - the type of noise calculation to use, c("percentile", "derivative", "combined").
p - numeric value between 0 and 1, the quantile used.
fact - numeric value, the factor by which the noise estimation was rised.
segN - was segN used TRUE or FASLE.
sn - the segmentation threshold.

Details

Produces a summary ".pdf" files containing various figures.

Value

PDF containing a "ProPlot", "GenomePlot" and two MAplots (MAplot1 and MAplot2).

Note

MA-plots a usful way of assessing the quality of the normalisation. Most points should be centered around zero and the outliers should have little effect on the overall fit (this is the key point of this normalisation method).

Author(s)

Tomas William Fitzgerald

Examples

# NA

[Package aCGH.Spline version 2.2 Index]