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

In rxmenezes/SIM: Integrated Analysis on two human genomic datasets

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

and c) “window” a percentage percentage significant window of length window

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

Details

details: Cytobands plot adapted from SNPChip

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 [e-mail]

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") 

rxmenezes/SIM documentation built on March 31, 2020, 12:51 a.m.