\name{sim.plot.pvals.on.region}
\alias{sim.plot.pvals.on.region}
\title{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 
  \code{input.regions}.
}
\usage{
sim.plot.pvals.on.region(input.regions = c("all chrs"), adjust.method = c("BY", "BH", "raw"), run.name = NULL, ...)
}

\arguments{
 \item{input.regions}{\code{\link{vector}} with analyzed regions for which to produce the graphs. 
  Can be defined in four ways:
  \code{1) predefined input region: } insert a predefined input region, choices are:
  \code{"all chrs"}, \code{"all chrs auto"}, \code{"all arms"}, \code{"all arms auto"}
  In the predefined regions \code{"all arms"} and \code{"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 \code{\link{vector}} of arms.
  \code{2) whole chromosome(s): }insert a single chromosome or a list of chromosomes as a \code{\link{vector}:}
  \code{c(1, 2, 3)}.
  \code{3) chromosome arms: } insert a single chromosome arm  or a list of chromosome arms like 
  \code{c("1q", "2p", "2q")}.
  \code{4) subregions of a chromosome: } insert a chromosome number followed by the start and end position
 like \code{c("chr1_1-1000000")}
  These regions can also be combined, e.g. \code{c("chr1_1-1000000","2q", 3)}.
  For more information see the \code{details} section of \code{\link{integrated.analysis}}.}  
  
  \item{adjust.method}{Method used to adjust the p-values for multiple
   testing. Either \code{"BY"} (recommended when copy number is used as dependent data), 
   \code{"BH"} or \code{"raw"}. Defaults to "BY". See \code{\link{SIM}} for more information about adjusti
ng p-values.}
  
\item{run.name}{Name of the analysis. The results will be 
   stored in a folder with this name in the current working directory 
   (use \code{getwd()} to print the current working directory). 
   If the \code{run.name = NULL}, the default folder \code{"analysis_results"} will be generated.}
\item{...}{Arguments to be passed to methods, such as graphical parameters (see \link{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 \code{run.name} as pdf.}

\author{Marten Boetzer, Melle Sieswerda, Renee X. de Menezes  \email{R.X.Menezes@lumc.nl}}

\seealso{
\code{\link{SIM}}, \code{\link{assemble.data}}, \code{\link{integrated.analysis}}, 
\code{\link{sim.plot.zscore.heatmap}}, \code{\link{sim.plot.pvals.on.genome}}, 
\code{\link{tabulate.pvals}}, \code{\link{tabulate.top.dep.features}}, 
\code{\link{tabulate.top.indep.features}}, \code{\link{impute.nas.by.surrounding}}, 
\code{\link{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")
}
\keyword{misc}