CNVMetrics: Copy Number Variant Metrics

calculateLog2ratioMetric

R Documentation

Calculate metric using overlapping amplified/deleted regions

Description

This function calculates a specific metric, as specified by the user, using overlapping amplified/deleted regions between to samples. The metric is calculated for the amplified and deleted regions separately. When more than 2 samples are present, the metric is calculated for each sample pair.

Usage

calculateLog2ratioMetric(
  segmentData,
  method = c("weightedEuclideanDistance"),
  minThreshold = 0.2,
  excludedRegions = NULL,
  nJobs = 1
)

Arguments

`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. This should be (an unambiguous abbreviation of) one of "weightedEuclideanDistance". Default: "weightedEuclideanDistance".
`minThreshold`	a single positive `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. Default: 0.2.
`excludedRegions`	an optional `GRanges` containing the regions that have to be excluded for the metric calculation. Default: `NULL`.
`nJobs`	a single positive `integer` specifying the number of worker jobs to create in case of distributed computation. Default: `1` and always `1` for Windows.

Details

The weighted euclidean distance is (\sum((x_i - y_i)^2 * log(nbrBases_i))^0.5 where x and y are the values of 2 samples for a specific segment i and nbrBases the number of bases of the segment i.

Value

an object of class "CNVMetric" which contains the calculated metric. This object is a list with the following components:

LOG2RATIO a lower-triangular matrix with the results of the selected metric on the log2ratio values for each paired samples. The value NA is present when the metric cannot be calculated. The value NA is also present in the top-triangular section, as well as the diagonal, of the matrix.

The object has the following attributes (besides "class" equal to "CNVMetric"):

metric the metric used for the calculation.
names the names of the two matrix containing the metrics for the amplified and deleted regions.

Author(s)

Astrid Deschênes, Pascal Belleau

Examples


## Load required package to generate the 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()
demo[["sample01"]] <- GRanges(seqnames="chr1",
    ranges=IRanges(start=c(1905048, 4554832, 31686841),
    end=c(2004603, 4577608, 31695808)), strand="*",
    log2ratio=c(2.5555, 1.9932, -0.9999))

demo[["sample02"]] <- GRanges(seqnames="chr1",
    ranges=IRanges(start=c(1995066, 31611222, 31690000),
    end=c(2204505, 31689898, 31895666)), strand=c("-", "+", "+"),
    log2ratio=c(0.3422, 0.5454, -1.4444))

## The amplified region in sample03 is a subset of the amplified regions
## in sample01
demo[["sample03"]] <- GRanges(seqnames="chr1",
    ranges=IRanges(start=c(1906069, 4558838),
    end=c(1909505, 4570601)), strand="*",
    log2ratio=c(3.2222, -1.3232))

## Calculating Sorensen metric
calculateLog2ratioMetric(demo, method="weightedEuclideanDistance", nJobs=1)

adeschen/CNVMetrics documentation built on July 19, 2023, 10:24 p.m.