calculateSorensen: Calculate Sorensen metric

In KrasnitzLab/CNVMetrics: Copy Number Variant Metrics

Calculate Sorensen metric

Description

Calculate Sorensen metric using overlapping regions between two samples.

Usage

calculateSorensen(sample01, sample02)

Arguments

sample01	a GRanges which contains a collection of genomic ranges representing copy number events for the first sample.
sample02	a GRanges which contains a collection of genomic ranges representing copy number events for the second sample.

Details

The method calculates the Sorensen metric using overlapping regions between the samples. All regions present in both samples are used for the calculation of the metric.

The Sorensen metric is calculated by dividing twice the size of the intersection by the sum of the size of the two sets. If the sum of the size of the two sets is zero; the value NA is returned instead. The strand of the regions is not taken into account while calculating the intersection.

Value

a numeric, the value of the Sorensen metric. If the metric cannot be calculated, NA is returned.

Author(s)

Astrid Deschênes

References

Sørensen, Thorvald. n.d. “A Method of Establishing Groups of Equal Amplitude in Plant Sociology Based on Similarity of Species and Its Application to Analyses of the Vegetation on Danish Commons.” Biologiske Skrifter, no. 5: 1–34.

Examples

## Load required package to generate the two samples
require(GenomicRanges)

## Generate two samples with identical sequence levels
sample01 <- GRanges(seqnames="chr1", 
    ranges=IRanges(start=c(1905048, 4554832, 31686841), 
    end=c(2004603, 4577608, 31695808)), strand="*")
sample02 <- GRanges(seqnames="chr1", 
    ranges=IRanges(start=c(1995066, 31611222), 
    end=c(2204505, 31689898)), strand="*")

## Calculate Sorensen metric    
CNVMetrics:::calculateSorensen(sample01=sample01, sample02=sample02)
    

KrasnitzLab/CNVMetrics documentation built on July 30, 2023, 2:22 p.m.