plotPolymorphicRegion: Plot polymorphic regions.

In CNVrd2: CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.

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. [e-mail]

See Also

identifyPolymorphicRegion

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)

CNVrd2 documentation built on Nov. 8, 2020, 5:30 p.m.