sim.plot.pvals.on.region {SIM} | R Documentation |
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.
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 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 |
run.name |
This must be the same a given to |
... |
Arguments to be passed to |
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”.
No values are returned. The results are stored in a subdirectory of run.name
as pdf.
Marten Boetzer, Melle Sieswerda, Renee X. de Menezes R.X.Menezes@lumc.nl
#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")