tabulate.pvals {SIM} | R Documentation |
Generates a data.frame
with the significance of P-values in the analyzed regions, dividing them into bins.
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 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. |
bins |
|
significance.idx |
Index of “bins” to use when computing the percentage of significant P-values. 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 p-values). |
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 P-values that is smaller or equal to the corresponding entry
in bins.
The last entry holds the percentage of P-values that is smaller than or
equal to the bin identified by significance.idx
.
Marten Boetzer, Melle Sieswerda, Renee X. de Menezes R.X.Menezes@lumc.nl
SIM, tabulate.top.dep.features, tabulate.top.indep.features
#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")