R: Plot polymorphic regions.

plotPolymorphicRegion {CNVrd2}

R Documentation

Plot polymorphic regions.

Description

Plot polymorphic regions based on coordinates set by users.

Usage

plotPolymorphicRegion(Object, ...)

Arguments

Object

An object of class CNVrd2

...

polymorphicRegionObjectAn object obtained from the process of identifying poplymorphic regions.

Optional arguments.

Value

putativeBoundary

Putative boundaries of polymorphic regions based on quantile values.

Note

Users can choose various quantile values and adjust different thresholds to obtain polymorphic regions.

Author(s)

Hoang Tan Nguyen, Tony R Merriman and MA Black. hoangtannguyenvn@gmail.com

Examples

## Not run: 

plotPolymorphicRegion(Object = objectCNVrd2, polymorphicRegionObject = fcgr3PolymorphicRegion,
                      xlim = c(161300000, 161800000), drawThresholds = TRUE,
                      thresholdForPolymorphicRegions = c(0.75, 0.25))



##Change thresholds
plotPolymorphicRegion(Object = objectCNVrd2, polymorphicRegionObject = fcgr3PolymorphicRegion,
                      xlim = c(161300000, 161800000), drawThresholds = TRUE,
                      thresholdForPolymorphicRegions = c(0.9, 0.1))


##Plot standard deviation

plotPolymorphicRegion(Object = objectCNVrd2, polymorphicRegionObject = fcgr3PolymorphicRegion,
                      xlim = c(161300000, 161800000), typePlot = "SD",
                      thresholdForPolymorphicRegions = c(0.75, 0.25))






## End(Not run)

[Package CNVrd2 version 1.26.0 Index]