calculateOneOverlapMetricT: Calculate metric using overlapping amplified/deleted regions...

In adeschen/CNVMetrics: Copy Number Variant Metrics

Calculate metric using overlapping amplified/deleted regions between two samples.

Description

Calculate a specific metric using overlapping amplified/deleted regions between two samples.

Usage

calculateOneOverlapMetricT(entry, segmentData, method, type)

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 'state' with a state, in an character string format, specified for each region (ex: DELETION, LOH, AMPLIFICATION, NEUTRAL, etc.).
method	a character string representing the metric to be used ('sorensen' or 'szymkiewicz'.
type	a character string representing the type of copy number events to be used ('AMPLIFICATION' or 'DELETION').

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 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, 32686222), 
    end=c(2004603, 4577608, 31695808, 32689222)), strand="*",
    state=c("AMPLIFICATION", "AMPLIFICATION", "DELETION", "LOH"))

demo[["sample02"]] <- GRanges(seqnames="chr1", 
    ranges= IRanges(start=c(1995066, 31611222, 31690000, 32006222), 
    end=c(2204505, 31689898, 31895666, 32789233)), 
    strand=c("-", "+", "+", "+"),
    state=c("AMPLIFICATION", "AMPLIFICATION", "DELETION", "LOH"))

## 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="*",
    state=c("AMPLIFICATION", "DELETION"))

## The 2 samples used to calculate the metric
entries <- data.frame(row=c(2, 3), col=c(1, 1))   

## Calculate Sorensen metric for the amplified regions on samples 2 and 3  
CNVMetrics:::calculateOneOverlapMetricT(entry=entries, segmentData=demo,
    method="sorensen", type="AMPLIFICATION")

## Calculate Szymkiewicz-Simpson metric for the amplified regions 
## in samples 1 and 2  
## Amplified regions of sample02 are a subset of the amplified 
## regions in sample01
CNVMetrics:::calculateOneOverlapMetricT(entry=entries, segmentData=demo,
    method="szymkiewicz", type="AMPLIFICATION")

## Calculate Sorensen metric for the deleted regions in samples 1 and 2  
CNVMetrics:::calculateOneOverlapMetricT(entry=entries, segmentData=demo,
    method="sorensen", type="DELETION")

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