calculateOneLog2valueMetricT: Calculate metric using the log2ratio values between two...

In KrasnitzLab/CNVMetrics: Copy Number Variant Metrics

Calculate metric using the log2ratio values between two samples.

Description

Calculate a specific metric using the level of amplification/deletion, in log2 ratio, between two samples.

Usage

calculateOneLog2valueMetricT(
  entry,
  segmentData,
  method,
  minThreshold,
  bedExclusion
)

Arguments

entry	a list which contains the row and column indexes (always in this order) of the metric in the final matrix. Those values correspond to the positions of the two samples used to calculate the metric in the GRangesList (segmentData).
segmentData	a GRangesList that contains a collection of genomic ranges representing copy number events, including amplified/deleted status, from at least 2 samples. All samples must have a metadata column called 'log2ratio' with the log2ratio values.
method	a character string representing the metric to be used ('weightedEuclideanDistance').
minThreshold	a single numeric setting the minimum value to consider two segments as different during the metric calculation. If the absolute difference is below or equal to threshold, the difference will be replaced by zero.
bedExclusion	an optional GRanges containing the regions that have to be excluded for the metric calculation or codeNULL.

Details

The method calculates a specified metric using overlapping regions between the samples. Only regions corresponding to the type specified by user are used in the calculation of the metric. The strand of the regions is not taken into account while calculating 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.

Value

a list containing 1 entry:

• metric a data.frame, which contains 3 columns. The 2 first columns, called row and column correspond to the indexes of the metric in the final matrix. Those 2 first columns match to the entry parameter. The third column, called metric, contains the values of the specified metric for each combination. If the metric cannot be calculated, NA is present.

Author(s)

Astrid Deschênes

Examples

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

## Create a GRangesList object with 3 samples
## The stand of the regions doesn't affect the calculation of the metric
demo <- GRangesList()

## Generate two samples with log2value information as a metadata column
demo[["sample01"]]  <- GRanges(seqnames="chr1", 
    ranges=IRanges(start=c(100, 201, 400), 
    end=c(200, 350, 500)), strand="*",
    log2ratio=c(1.1111, 2.2222, -0.9999))
demo[["sample02"]] <- GRanges(seqnames="chr1", 
    ranges=IRanges(start=c(150, 200, 450), 
    end=c(250, 350, 500)), strand="*",
    log2ratio=c(2.2121, 1.1212, -1.3939))

## The 2 samples used to calculate the metric
entries <- data.frame(row=c(2), col=c(1)) 

## Calculate weighted Euclidean distance 
CNVMetrics:::calculateOneLog2valueMetricT(entry=entries, 
    segmentData=demo, method="weightedEuclideanDistance", 
    minThreshold=0.2, bedExclusion=NULL)

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