chromothripsis: CNomplexity::chromothripsis

In SteeleCD/CNomplexity: Analysis of Complex Copy Cumber and Structural Variants in Cancer Genomes.

Description

Identify chromothriptic regions.

Usage

chromothripsis(bedpeFile, size=3e7,
			gap=1e6,
			bedpeChromCol1=1,bedpePosCol1=2,direction1col=9,
			bedpeChromCol2=4,bedpePosCol2=5,direction2col=10,
			bedpeSampleCol=1,svclassCol=NULL,
			doParallel=FALSE,
			nCores = NULL,samplesToRun = NULL,
			chromsToRun = NULL,sepbedpe=TRUE,
			bedpeHead=FALSE,bedpeEnding=".brass.annot.bedpe.gz",
			breaksLimit=30,pThresh=0.8,
			cytoFile=NULL,
			diag=FALSE)

Arguments

bedpeFile	Directory of separate bedpe files, or filename of single bedpe file.
size	Window size for sliding window across chomosomes.
gap	Gap between consecutive sliding windows.
bedpeChromCol1	Column of bedpe file with chromosome name for first fusion partner.
bedpePosCol1	Column of bedpe file with position for first fusion partner.
direction1col	Column of bedpe file with orientation for first fusion partner.
bedpeChromCol2	Column of bedpe file with chromosome name for second fusion partner.
bedpePosCol2	Column of bedpe file with position for second fusion partner.
direction2col	Column of bedpe file with orientation for second fusion partner.
bedpeSampleCol	Column of bedpe file with sample name.
svclassCol	Column of structural variation class e.g. deletion, inversion, tandem-duplication or translocation
doParallel	Whether to run in parallel
nCores	Number of cores if doParallel=TRUE.
samplesToRun	Character vector with sample names to run analysis for.
chromsToRun	Character vector with chromosome names to run analysis for.
sepbedpe	Whether bedpe files are separate or concatenated.
bedpeHead	Whether bedpe file has a header.
bedpeEnding	File ending for separate bedpe files.
breaksLimit	Minimum number of breakpoints on a chromsome to consider chromothripsis. Defaults to 30.
pThresh	P value threshold for test of randomness (random order of breakpoints and random joins). Defaults to 0.8.
cytoFile	File with starts and ends of chromosome bands. If NULL defaults to a file supplied with CNomplexity.
diag	Boolean. Whether to return diagnostic outputs.

Details

Implements three tests from Korbel & Campbell (2013).

Value

List of samples and chromosmores, with each element being a matrix with Sample name, start positon of chromothriptic region and end position of chromothriptic region. NULL is no chromothriptic regions in the chromosome.

SteeleCD/CNomplexity documentation built on May 29, 2019, 2:09 p.m.