sim.plot.pvals.on.genome: Plot the P-values in whole genome overview

In SIM: Integrated Analysis on two human genomic datasets

Description

Generates a plot of the analyzed dependent data probe positions and their significance on all chromosomes.

Usage

sim.plot.pvals.on.genome(input.regions = "all chrs", 
  					     significance = c(0.05, 0.20), 
						 adjust.method = "BY", 
						 method = c("full", "smooth", "window", "overlap"),		
						 run.name = "analysis_results",
						 pdf = TRUE, 
						 main = "Significantly associated features",
						 ylab = "Chromosomes",						 
						 ann=par("ann"),
						 ...)

Arguments

input.regions	vector indicating the dependent regions to be analyzed. Can be defined in four ways: 1) predefined input region: insert a predefined input region, choices are: “all chrs”, “all chrs auto”, “all arms”, “all arms auto” In the predefined regions “all arms” and “all arms auto” the arms 13p, 14p, 15p, 21p and 22p are left out, because in most studies there are no or few probes in these regions. To include them, just make your own vector of arms. 2) whole chromosome(s): insert a single chromosome or a list of chromosomes as a vector: c(1, 2, 3). 3) chromosome arms: insert a single chromosome arm or a list of chromosome arms like c("1q", "2p", "2q"). 4) subregions of a chromosome: insert a chromosome number followed by the start and end position like "chr1:1-1000000" These regions can also be combined, e.g. c("chr1:1-1000000","2q", 3). See integrated.analysis for more information.
significance	Two values that categorize the P-values on the selected chromosomes. These margins are indicated by different colors shown in the legend. These values can be defined, e.g. pval.sig = c(0.3, 0.075)
adjust.method	Method used to adjust the P-values for multiple testing. see p.adjust Default is “BY” recommended when copy number is used as dependent data. See SIM for more information about adjusting P-values.
method	this must be the either full, window, overlap or smooth but the data should generated by the same method in integrated.analysis.
pdf	Boolean. Indicate whether to generate a pdf of the plots in the current working directory or not.
run.name	This must be the same a given to integrated.analysis
main	the usual graphical parameter for the caption of the plot.
ylab	the usual graphical parameter for the y-axis label of the plot.
ann	the usual graphical parameter for annotation of the plot.
...	Arguments to be passed to pdf when pdf = TRUE, see Details.

Details

Grey vertical lines indicate unsignificant probes on top the significant ones are plotted. A purple dot indicates the centromere and a organe line the input region.

Sometimes it is useful to make the genome-plot as A4 landscape-format, add the following parameters to the sim.plot.pvals.on.genome(..., paper='a4r', width=0, height=0)

Value

No values are returned. The results are stored in the folder “pvalue.plots” in directory run.name as pdf.

Author(s)

Marten Boetzer, Melle Sieswerda, Renee X. de Menezes [e-mail]

See Also

SIM, sim.plot.zscore.heatmap, sim.plot.pvals.on.region

Examples

#first run example(assemble.data)
#and example(integrated.analysis)
#plot the p-values along the genome
sim.plot.pvals.on.genome(input.regions="8q", 
		                 significance=c(0.05, 0.005), 
						 adjust.method="BY", 
						 method="full", 
						 pdf=FALSE, 
						 run.name="chr8q")

SIM documentation built on Nov. 8, 2020, 4:58 p.m.