ivg_sv: Interactive exploration of SVs in a variation graph

View source: R/ivg_sv.R

ivg_svR Documentation

Interactive exploration of SVs in a variation graph

Description

Opens a Shiny app with a dynamic table that contains input SVs. Clicking on a SV (row in the table) generates a simplified representation of the variation graph around this SV. The number of flanking nodes (context) can be increased if necessary, e.g. for large insertions. vg needs to be installed (https://github.com/vgteam/vg).

Usage

ivg_sv(svs, xg, ucsc.genome = "hg38")

Arguments

svs

either a GRanges with SVs (e.g. from readSVvcf) or the path to a VCF file.

xg

the path to the xg object of the variation graph.

ucsc.genome

the genome version for the UCSC Genome Browser automated link.

Value

Starts a Shiny app in a web browser.

Author(s)

Jean Monlong


jmonlong/sveval documentation built on July 31, 2023, 7:50 p.m.