identifyPolymorphicRegion: Identity 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

Using quantile values to identify polymorphic regions.

Usage

identifyPolymorphicRegion(Object, ...)

Arguments

Object	An object of class CNVrd2
...	polymorphicRegionObjectAn object obtained from the process of identifying poplymorphic regions. Optional arguments.

Value

putativeBoundary	resultant boundaries based on quantile thresholds.
subRegionMatrix	segmentation-score matrix of sub-regions derived from the segmentation process.
subRegion	sub-regions derived from the segmentation process.
mQuantile	matrix of quantile values.
mSD	data frame including subregions and their standard deviations.
Vst	data frame of Vst between populations if VstTest = TRUE.
SSofPolymorphicRegions	segmentation scores of polymorphic regions.

Note

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

To visualize more clearly polymorphic regions user can use the method plotPolymorphicRegion with the option typePlot="SD".

Author(s)

Hoang Tan Nguyen, Tony R Merriman and MA Black. [e-mail]

See Also

plotPolymorphicRegion

Examples

## Not run: 

fcgr3PolymorphicRegion <- identifyPolymorphicRegion(Object = objectCNVrd2,
                                                    segmentObject = resultSegment, 
                                                    thresholdForPolymorphicRegions = c(0.75, 0.25),
                                                    plotLegend = FALSE)



## End(Not run)

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