CNVassoc (version 2.2)

plotSignal: plots the intensities of a CNV univariate signal data

Description

This function creates a plot with probe intensity

Usage

plotSignal(x, my.colors = c("black", "red", "blue"), ylab = "Peak Intensity",  xlab = c("individuals", "Phenotype"), case.control = NULL, cex.leg = 0.6,  dens.bw = "nrd0", dens.adjust = 1, n = 0, ...)

Arguments

x

A vector with probe intensities

my.colors

Colours for each copy number status.

ylab

Label of y-axis

xlab

Label of x-axis

case.control

Vector indicating case-control status

cex.leg

Size of legend

dens.bw

Adjustment for intensity signal density curve. See argument 'bw' of density function for more details

dens.adjust

Adjustment for intensity signal density curve. See argument 'adjust' of density function for more details

n

integer indicating the number of points to be placed on the plot interactively (using locator)) to define the thresholds that separate the different copy number status, colouring the points differently according to the assigned copy number status. If it zero or negative it makes no possible to place the threshold points.

...

Other arguments passed to plot.default

Details

See vignette for further description

References

Gonzalez JR, Subirana I, Escaramis G, Peraza S, Caceres A, Estivill X and Armengol L. Accounting for uncertainty when assessing association between copy number and disease: a latent class model. BMC Bioinformatics, 2009;10:172.

See Also

cnv

Examples

data(dataMLPA)
plotSignal(dataMLPA$Gene2)