sim.plot.pvals.on.region {SIM} | R Documentation |
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
.
sim.plot.pvals.on.region(input.regions = c("all chrs"), adjust.method = c("BY", "BH", "raw"), run.name = NULL, ...)
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). |
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".
No values are returned. The results are stored in a subdirectory of run.name
as pdf.
Marten Boetzer, Melle Sieswerda, Renee X. de Menezes R.X.Menezes@lumc.nl
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
#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")