SIM (version 1.42.0)

sim.plot.overlapping.indep.dep.features: P-value plot and mean-zscore plots with indication of overlapping features.

Description

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.

Usage

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", ...)

Arguments

input.regions

vector indicating the dependent regions to be analyzed. 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 "chr1:1-1000000" These regions can also be combined, e.g. c("chr1:1-1000000","2q", 3). See integrated.analysis for more information.

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

logical default log = FALSE, if log = TRUE P-values are plotting on $log[10]$ scale.

significance

The threshold for selecting significant P-values.

max.pow

numeric only when log = TRUE scale of the y-axis.

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 z.threshold (high positive association) or below -z.threshold (high negative association).

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 percentage significant stretch of size stretch

stretch

integer length of stretch, default stretch = 10

window

integer length of window, default window = 1e6

percentage

numeric a number between $[0,1]$ given the percentage of significance in either the “stretch” of “window”

xlim

c(min, max) scale of the x-axis. Can be used for zooming in on a region.

pdf

logical indicate whether to generate a pdf of the plots in the current working directory or not.

method

this must be the either full, window, overlap or smooth but the data should generated by the same method in integrated.analysis.

run.name

This must be the same a given to integrated.analysis

...

not used in this version

Value

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

Details

details: Cytobands plot adapted from SNPChip

See Also

SIM, tabulate.top.dep.features, tabulate.top.indep.features, getoverlappingregions

Examples

#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")