LINX

2023-08-22

require(gpgr)
require(devtools)
require(dplyr)
require(knitr)
require(DT)

Introduction

LINX: annotation, interpretation and visualisation tool for structural variants.

• https://github.com/hartwigmedical/hmftools/tree/master/linx.
• groups SV calls together into events
• inputs: GRIDSS SVs, PURPLE CNVs, gene panel, known fusions/fragile sites/LINEs

Table Outputs

Annotations

• additional annotations of each non PON filtered break junction
• svs.tsv

system.file("extdata/linx/tables/linx.svs.tsv.gz", package = "gpgr") |>
  gpgr::linx_svs_read() |>
  dt_table_random10()

Breakends

• impact of each non PON filtered break junction on each overlapping gene
• breakend.tsv

system.file("extdata/linx/tables/linx.breakend.tsv.gz", package = "gpgr") |>
  gpgr::linx_breakend_read() |>
  dt_table_random10()

Clusters

• clustering of all non PON filtered SV events and their resolved classification.
• clusters.tsv

system.file("extdata/linx/tables/linx.clusters.tsv.gz", package = "gpgr") |>
  gpgr::linx_clusters_read() |>
  dt_table_random10()

Links

• segments joining break junction pairs predicted to be linked and phased in cis on the derivative chromosome.
• links.tsv

system.file("extdata/linx/tables/linx.links.tsv.gz", package = "gpgr") |>
  gpgr::linx_links_read() |>
  dt_table_random10(n = 1)

Fusions

• All inframe and outframe fusions predicted in the sample including HMF fusion knowledgebase annotations.
• fusion.tsv

system.file("extdata/linx/tables/linx.fusion.tsv.gz", package = "gpgr") |>
  gpgr::linx_fusion_read() |>
  dt_table_random10()

Driver Catalog

• Reproduction of the driver catalog produced by PURPLE with homozygous disruption events appended.
• driver.catalog.tsv

system.file("extdata/linx/tables/linx.driver.catalog.tsv.gz", package = "gpgr") |>
  gpgr::linx_drivercatalog_read() |>
  dt_table_random10()

Drivers

• Linkage of drivers from driver catalog to SV cluster which contributed to those drivers including LOH, deletion, disruption and amplification events.
• drivers.tsv

system.file("extdata/linx/tables/linx.drivers.tsv.gz", package = "gpgr") |>
  gpgr::linx_drivers_read() |>
  dt_table_random10()

Viral Inserts (Not Documented)

Table ‘vis’ outputs

Copy Number

• linx.vis_copy_number.tsv

system.file("extdata/linx/tables/linx.vis_copy_number.tsv.gz", package = "gpgr") |>
  gpgr::linx_viscopynumber_read() |>
  dt_table_random10()

Fusion

• linx.vis_fusion.tsv

system.file("extdata/linx/tables/linx.vis_fusion.tsv.gz", package = "gpgr") |>
  gpgr::linx_visfusion_read() |>
  dt_table_random10(n = 1)

Gene Exon

• linx.vis_gene_exon.tsv

system.file("extdata/linx/tables/linx.vis_gene_exon.tsv.gz", package = "gpgr") |>
  gpgr::linx_visgeneexon_read() |>
  dt_table_random10()

Protein Domain

• linx.vis_protein_domain.tsv

system.file("extdata/linx/tables/linx.vis_protein_domain.tsv.gz", package = "gpgr") |>
  gpgr::linx_visproteindomain_read() |>
  dt_table_random10()

Segments

• linx.vis_segments.tsv

system.file("extdata/linx/tables/linx.vis_segments.tsv.gz", package = "gpgr") |>
  gpgr::linx_vissegments_read() |>
  dt_table_random10()

SV Data

• linx.vis_sv_data.tsv

system.file("extdata/linx/tables/linx.vis_sv_data.tsv.gz", package = "gpgr") |>
  gpgr::linx_vissvdata_read() |>
  dt_table_random10()

Session Info

Main packages used in this vignette.

package	version	datestamp	source
base	4.2.3	2023-07-13	local
gpgr	1.5.0	2023-08-22	local

Platform information.

name	value
version	R version 4.2.3 (2023-03-15)
os	Ubuntu 22.04.3 LTS
system	x86_64, linux-gnu
ui	X11
language	en
collate	C.UTF-8
ctype	C.UTF-8
tz	Etc/UTC
date	2023-08-22
pandoc	3.1.3 @ /home/runner/micromamba/envs/pkgdownenv/bin/ (via rmarkdown)