upstream_partner_gene: Get the upstream fusion partner gene

In stianlagstad/chimeraviz: Visualization tools for gene fusions

Get the upstream fusion partner gene

Description

This getter retrieves the upstream PartnerGene object.

This sets the upstream PartnerGene object of a Fusion object

Usage

upstream_partner_gene(x)

## S4 method for signature 'Fusion'
upstream_partner_gene(x)

upstream_partner_gene(object) <- value

## S4 replacement method for signature 'Fusion'
upstream_partner_gene(object) <- value

Arguments

x	The Fusion object you wish to retrieve the upstream PartnerGene object for.
object	The Fusion object you wish to set a new upstream PartnerGene object for.
value	The new PartnerGene object.

Value

The upstream PartnerGene object.

Examples

# Load data
defuseData <- system.file(
  "extdata",
  "defuse_833ke_results.filtered.tsv",
  package="chimeraviz")
fusions <- import_defuse(defuseData, "hg19", 1)
fusion <- fusions[[1]]
# Get the upstream fusion partner gene
upstream_partner_gene(fusion)

# Load data
defuseData <- system.file(
  "extdata",
  "defuse_833ke_results.filtered.tsv",
  package="chimeraviz")
fusions <- import_defuse(defuseData, "hg19", 1)
fusion <- fusions[[1]]
# Set the upstream PartnerGene object to be the same as the downstream
# PartnerGene object
upstream_partner_gene(fusion) <- downstream_partner_gene(fusion)

stianlagstad/chimeraviz documentation built on Dec. 3, 2023, 8:11 p.m.