Description Usage Arguments Value Author(s) See Also Examples
View source: R/tabulate.pvals.R
Generates a data.frame
with the significance of Pvalues in the analyzed regions, dividing them into bins.
1 2 3 4 5 6 7 8  tabulate.pvals(input.regions = "all chrs",
adjust.method = "BY",
bins = c(0.001, 0.005, 0.01, 0.025, 0.05, 0.075, 0.1, 0.2, 1),
significance.idx = 8,
order.by,
decreasing = TRUE,
method = c("full", "smooth", "window", "overlap"),
run.name = "analysis_results")

input.regions 

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. 
bins 

significance.idx 
Index of “bins” to use when computing the percentage of significant Pvalues. Defaults to 8 (i.e. the first entry in “bins”), in this case 0.20. 
order.by 
Column used for sorting the table. Defaults to "%" (i.e. the percentage of significant pvalues). 
decreasing 
Direction used for sorting. Defaults to TRUE (i.e. highest values on top). 
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 
Returns a data.frame
. Each row corresponds to a chromosome and has
as many entries as entries in bins, plus 1. Each entry contains the
number of Pvalues that is smaller or equal to the corresponding entry
in bins.
The last entry holds the percentage of Pvalues that is smaller than or
equal to the bin identified by significance.idx
.
Marten Boetzer, Melle Sieswerda, Renee X. de Menezes [email protected]
SIM, tabulate.top.dep.features, tabulate.top.indep.features
1 2 3 4 5 6  #first run example(assemble.data)
#and example(integrated.analysis)
tabulate.pvals(input.regions="8q",
adjust.method="BY",
bins=c(0.001,0.005,0.01,0.025,0.05,0.075,0.10,0.20,1.0),
run.name="chr8q")

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