plot.WGassociation: Function to plot -log p values from an object of class 'WGassociation'

Description

Function to plot -log p values from an object of class 'WGassociation'

Usage

## S3 method for class 'WGassociation':
plot(x, alpha = 0.05, plot.all.SNPs = FALSE, 
  print.label.SNPs = TRUE, cutPval = c(0, 1e-10, 1), whole, 
  ylim.sup=ifelse(is.null(attr(x,"fast")),1e-40, 1e-30),  
  col.legend = c("red", "gray60"), sort.chromosome=TRUE, 
  centromere, ...)

Arguments

an object of class 'WGassociation'

alpha

statistical significance nominal level. See details

plot.all.SNPs

are all SNPs plotted? If not, neither monomorphic nor SNPs with genotyping problems are plotted. The default is FALSE.

print.label.SNPs

are labels of SNPs printed? The default is TRUE

cutPval

when argument 'whole' is TRUE in the 'x' object (e.g. when whole genome analysis is carried out) 'cutPval divides the range of p values into intervals and codes these values according to which interval they fall (like 'cut' funct

whole

is a whole genome carried out? If TRUE 'dataSNPs.pos' argument in 'setupSNP' is required.

ylim.sup

superior limit for each panel. This value helps to obtain nicer plots

col.legend

the color of the bar corresponding to p values plotted in each panel. The default is "red" for those p values less than 1e-10 and "gray60" for those greater than 1e-10.

sort.chromosome

should chromosome be sorted? Set this argument to FALSE when genomic information corresponds to different genes.

centromere

numeric vector specifying the centromere positions. If missing, the default centromere value of human genome are used.

...

other graphical parameters

Value

No return value, just the plot

Details

A panel with different plots (one for each mode of inheritance) are plotted. Each of them represents the -log(p value) for each SNP. Two horizontal lines are also plotted. One one them indicates the nominal statistical significance level (see 'alpha' argument) whereas the other one indicates the statistical significance level after Bonferroni correction. A different plot is created when the argument 'whole' the object 'x' is TRUE (see setupSNP function). In that case a plot of p values in the -log sclae is plotted for each SNP and for each chromosome.

References

JR Gonzalez, L Armengol, X Sole, E Guino, JM Mercader, X Estivill, V Moreno. SNPassoc: an R package to perform whole genome association studies. Bioinformatics, 2007;23(5):654-5.