plotSignal: plots the intensities of a CNV univariate signal data

In isglobal-brge/CNVassoc: Association analysis of CNVs and imputed SNPs incorporating uncertainty

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

Value

This function produces a plot and returns the coordenates introduced by the user with locator when n>0.

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)

isglobal-brge/CNVassoc documentation built on May 30, 2019, 9:48 p.m.