svType: Determines the structural variant type

In cancer-genomics/plasmasv: Methods for identification of tumor-specific structural variants in plasma

Description

Determines the structural variant type

Usage

svType(x)

Arguments

x	A GRanges object containing breakpoint 1 with a GRanges for breakpoint 2 in a metadata column caled linked.to

Details

For intrachromosomal events, it is expected that the position of breakpoint 1 is less than the position of breakpoint 2. When the chromosome is not the same, the SV is assigned 'TRA', when the chromosome is the same, it is assgned 'INV' if the strands are ++ or –, 'DEL' if the strands are +-, and 'DUP' if the strands are -+.

Examples

Example 1: Determining the structural variant type for each rearrangement in test_sv
data(test_sv)
svType(test_sv)

cancer-genomics/plasmasv documentation built on May 15, 2020, 11:35 a.m.