partner_gene_ensembl_id: Get the Ensembl ID from a PartnerGene object

In stianlagstad/chimeraviz: Visualization tools for gene fusions

Get the Ensembl ID from a PartnerGene object

Description

This getter retrieves the Ensembl ID from a PartnerGene object

This sets the Ensembl ID of a PartnerGene object.

Usage

partner_gene_ensembl_id(x)

## S4 method for signature 'PartnerGene'
partner_gene_ensembl_id(x)

partner_gene_ensembl_id(object) <- value

## S4 replacement method for signature 'PartnerGene'
partner_gene_ensembl_id(object) <- value

Arguments

x	The PartnerGene object you wish to retrieve the Ensembl ID for.
object	The PartnerGene object you wish to set a new Ensembl ID for.
value	The new Ensembl ID.

Value

The upstream fusion partner gene Ensembl ID.

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 Ensembl ID from the upstream fusion partner gene
partner_gene_ensembl_id(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 downstream PartnerGene object to be the same as the upstream
# PartnerGene object
partner_gene_ensembl_id(upstream_partner_gene(fusion)) <- "test"

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