Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/sim.plot.pvals.on.region.R
Generates two plots of the Pvalues for an analyzed region. The first plot contains the distribution of the raw Pvalues and ranked plots of the raw and adjusted Pvalues. The second plot contains the Pvalues along the genome of analyzed input regions.
1 2 3 4 5  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", ...)

input.regions 

significance 
The threshold for selecting significant Pvalues. 
adjust.method 
Method used to adjust the Pvalues 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 Pvalues. 
method 
this must be the either full, window, overlap or smooth but the data should generated by the
same method in 
run.name 
This must be the same a given to 
... 
Arguments to be passed to 
This function returns a pdf containing the Pvalue plots. The second plot contains the multiple testing corrected Pvalues plotted along the chromosome (arm). On the xaxis, the start positions of the dependent features are displayed. On the yaxis, the Pvalue levels are displayed. Two dotted lines indicate Pvalue levels 0.2 and 0.1. In general, Pvalues below 0.2 are said to be “significant”.
No values are returned. The results are stored in a subdirectory of run.name
as pdf.
Marten Boetzer, Melle Sieswerda, Renee X. de Menezes [email protected]
SIM, sim.plot.pvals.on.genome
1 2 3 4 5 6 7  #first run example(assemble.data)
#and example(integrated.analysis)
#plot the pvalues along the regions
sim.plot.pvals.on.region(input.regions="8q",
adjust.method="BY",
method="full",
run.name="chr8q")

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