fusion_standardization: Standardizes fusion calls

Description Usage Arguments Value Examples

View source: R/fusion_standardization.R

Description

Various fusion callers have different formats that make aggregating and filtering data difficult. By standardizing fusion callers output we capture the required columns which we use for downstream analysis

Usage

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fusion_standardization(
  fusion_calls,
  caller = c("STARFUSION", "ARRIBA"),
  tumorID = "tumorID"
)

Arguments

fusion_calls

A dataframe from star fusion or arriba (more callers to be added)

caller

string options STARFUSION/ARRIBA

tumorID

string or character vector of same length as fusion_calls

Value

Standardized fusion calls ready for filtering

Examples

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# read in arriba fusion file
fusionfileArriba <- read_arriba_calls(
  system.file("extdata", "arriba_example.tsv", package = "annoFuseData")
)
# read in starfusion file
fusionfileStarFusion <- read_starfusion_calls(
  system.file("extdata", "starfusion_example.tsv", package = "annoFuseData")
)
formattedArriba <- fusion_standardization(fusionfileArriba,
  caller = "ARRIBA",
  tumorID = "tumorID"
)
formattedStarFusion <- fusion_standardization(fusionfileStarFusion,
  caller = "STARFUSION",
  tumorID = "tumorID"
)

d3b-center/annoFuse documentation built on March 11, 2021, 9:05 p.m.