sim.plot.pvals.on.region {SIM}R Documentation

P-value histograms and p-values along the genome per region

Description

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.

Usage

sim.plot.pvals.on.region(input.regions = c("all chrs"), adjust.method = c("BY", "BH", "raw"), run.name = NULL, ...)

Arguments

input.regions vector with analyzed regions for which to produce the graphs. Can be defined in four ways: 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). For more information see the details section of integrated.analysis.
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 adjusti ng 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.
... Arguments to be passed to methods, such as graphical parameters (see par).

Details

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".

Value

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

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.genome, tabulate.pvals, tabulate.top.dep.features, 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 = c(8), adjust=FALSE, zscores=TRUE, method = "auto", run.name= "chr8")

# use functions to plot the results of the integrated analysis

#plot the p-values along the region
sim.plot.pvals.on.region(input.regions = c(8), adjust.method="BY", run.name = "chr8")

[Package SIM version 1.10.0 Index]