tabulate.top.dep.features {SIM}R Documentation

Lists the p-values for the dependent features

Description

Lists the integrated analysis p-values for the dependent features in the analyzed regions, together with the available annotation.

Usage

tabulate.top.dep.features(input.regions = "all chrs", adjust.method = c("BY", "BH", "raw"), run.name = NULL)

Arguments

input.regions vector indicating the regions to be analyzed. Can be defined in four w ays: 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 c("chr1_1-1000000") These regions can also be combined, e.g. c("chr1_1-1000000","2q", 3). See details for more information.
adjust.method Method used to adjust the p-values for multiple testing. Either "BY" (recommended when copy number is used as dependent data), "BH" or "raw". Defaults to "BY". See SIM for more information about adjustin g p-values.
run.name Name of the analysis. The results will be stored in a folder with this name in the current working directory (use getwd() to print the current working directory). If the run.name = NULL, the default folder "analysis_results" will be generated.

Details

Output is a .txt file containing a table with sorted integrated analysis p-values of the dependent features. It includes the ann.dep columns that were read in the assemble.data function.

Value

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

Author(s)

Marten Boetzer, Melle Sieswerda, Renee X. de Menezes R.X.Menezes@lumc.nl

See Also

SIM, assemble.data, integrated.analysis, sim.plot.zscore.heatmap, sim.plot.pvals.on.region, sim.plot.pvals.on.genome, tabulate.pvals, tabulate.top.indep.features, impute.nas.by.surrounding, sim.update.chrom.table

Examples

#load the datasets and the samples to run the integrated analysis
data(expr.data)
data(acgh.data)
data(samples) 
         
#assemble the data
assemble.data(dep.data = acgh.data, indep.data = expr.data, ann.dep = colnames(acgh.data)[1:4], ann.indep = colnames(expr.data)[1:4], dep.id="ID",dep.chr = "CHROMOSOME",dep.pos = "STARTPOS",dep.symb="Symbol", indep.id="ID",indep.chr = "CHROMOSOME", indep.pos = "STARTPOS", indep.symb="Symbol", overwrite = TRUE,run.name = "chr8")

#run the integrated analysis
integrated.analysis(samples = samples, input.regions = 8, adjust=FALSE, zscores=TRUE, method = "auto", run.name = "chr8")

#get the top dependent features with lowest p-value
tabulate.top.dep.features(input.regions = 8, adjust.method="BY",run.name = "chr8")

[Package SIM version 1.10.0 Index]