sim.plot.pvals.on.region: P-value histograms and P-values along the genome per region

In SIM: Integrated Analysis on two human genomic datasets

Description

Generates two plots of the P-values for an analyzed region. The first plot contains the distribution of the raw P-values and ranked plots of the raw and adjusted P-values. The second plot contains the P-values along the genome of analyzed input regions.

Usage

sim.plot.pvals.on.region(input.regions = c("all chrs"),
						 significance = 0.2,	 
                         adjust.method = "BY",  
                         method = c("full", "smooth", "window", "overlap"),  
                         run.name = "analysis_results", ...)

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	The threshold for selecting significant P-values.
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.
run.name	This must be the same a given to integrated.analysis
...	Arguments to be passed to pdf.

Details

This function returns a pdf containing the P-value plots. The second plot contains the multiple testing corrected P-values plotted along the chromosome (arm). On the x-axis, the start positions of the dependent features are displayed. On the y-axis, the P-value levels are displayed. Two dotted lines indicate P-value levels 0.2 and 0.1. In general, P-values below 0.2 are said to be “significant”.

Value

No values are returned. The results are stored in a subdirectory of run.name as pdf.

Author(s)

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

See Also

SIM, sim.plot.pvals.on.genome

Examples

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

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