processChr: TODO

In KrasnitzLab/CNVMetrics: Copy Number Variant Metrics

TODO

Description

TODO

Usage

processChr(curSample, simChr, chrCur)

Arguments

curSample	a GRanges that contains a collection of genomic ranges representing copy number events, including amplified/deleted status, from one sample. The sample 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.) and a metadata column called 'CN' that contains the log2 copy number ratios.
simChr	a data.frame containing the information from one simulated chromosome (shuffled segments). The starting position and the ending position of the segments should be between zero and one. The segment width is representing the proportional size of the segment relative to the global segment size for the chromosome.The data.frame columns names should be: 'ID', 'chr', 'start', 'end', 'log2ratio', 'state'.
chrCur	a character string representing the name of the chromosome.

Details

TODO

Value

df TODO

Author(s)

Astrid Deschênes, Pascal Belleau

Examples

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

## Create one 'demo' genome with 2 chromosomes and few segments
## The stand of the regions doesn't affect the calculation of the metric
sample01 <- GRanges(seqnames=c(rep("chr1", 4), rep("chr2", 3)),
    ranges=IRanges(start=c(1905048, 4554832, 31686841, 32686222,
        1, 120331, 725531),
    end=c(2004603, 4577608, 31695808, 32689222, 117121,
        325555, 1225582)),
    strand="*",
    state=c("AMPLIFICATION", "NEUTRAL", "DELETION", "LOH",
        "DELETION", "NEUTRAL", "NEUTRAL"),
    log2ratio=c(0.5849625, 0, -1, -1, -0.87777, 0, 0))

## The simulated chromosome with shuffled segment
## The simulated chromosome can be a different chromosome
simulatedChr <- data.frame(ID=rep("S4", 4),
    chr=rep("chr2", 4), start=c(0, 0.02515227, 0.09360992, 0.25903561),
    end=c(0.02515227, 0.09360992, 0.25903561, 1),
    log2ratio=c(-1.0, -0.9999, 0.0, 0.5843),
    state=c("LOH", "DELETION", "NEUTRAL", "AMPLIFICATION"))

## Generates a simulation for chromosome 1 using a simulated chromosome
## The segments from the simulated chromosome will be positioned on the
## chromosome 1 after resizing for the size of chromosome 1.
## The spaces between the segments in chromosome 1 will be
## preserved.
CNVMetrics:::processChr(curSample=sample01, simChr=simulatedChr,
    chrCur="chr1")

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