sim.plot.overlapping.indep.dep.features {SIM} | R Documentation |
Generates three plots: The first plot contains the P-values along the region, with the cut-off displayed. The second plot contains the mean-zscores along the region, with the cut-offs displayed. The third plots generates the cytobands of the region.
sim.plot.overlapping.indep.dep.features(input.regions, input.region.indep = NULL, adjust.method = "BY", log = FALSE, significance = 0.2, max.pow = 5, z.threshold = c(-3,3), summarize = c("consecutive", "stretch", "window"), stretch = 10, window = 1e6, percentage = 0.5, xlim=NULL, pdf = FALSE, method = c("full", "smooth", "window", "overlap"), run.name = "analysis_results", ...)
input.regions |
|
input.region.indep |
indicating the independent region which will be analysed in combination of the dependent region. Only one input region can given using the same format as the dependent input region. |
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. |
log |
|
significance |
The threshold for selecting significant P-values. |
max.pow |
|
z.threshold |
Threshold to display a green or red bar in the color bar on top of
the heatmap for independent features with mean z-scores above |
summarize |
either one of “consecutive”, “stretch”, “window” which visualizes the subregions according to
the selected summarization a) “consecutive” shows the consecutive significant regions b) “stretch” shows
a percentage |
and c) “window” a percentage percentage
significant window of length window
stretch |
|
window |
|
percentage |
|
xlim |
|
pdf |
|
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 |
... |
not used in this version |
details: Cytobands plot adapted from SNPChip
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, tabulate.top.dep.features, tabulate.top.indep.features, getoverlappingregions
#first run example(assemble.data) #and example(integrated.analysis) #overview plot of the dependent and independent features sim.plot.overlapping.indep.dep.features(input.regions="8q", adjust.method="BY", significance=0.1, z.threshold= c(-1,1), log=TRUE, summarize="consecutive", pdf=FALSE, method="full", run.name="chr8q")