aggregate_fusion_calls: Function to aggregate Caller and read support per fusions...

Description Usage Arguments Value Examples

View source: R/aggregate_fusion_calls.R

Description

Function to aggregate Caller and read support per fusions calls

Usage

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aggregate_fusion_calls(standardFusioncalls, removeother = FALSE, filterAnnots)

Arguments

standardFusioncalls

A dataframe from star fusion or arriba standardized to run through the filtering steps

removeother

TRUE to remove Fusion_Type="other" and keep only in-frame and frameshift Default: FALSE

filterAnnots

regex to remove from annots column eg. LOCAL_REARRANGEMENT|LOCAL_INVERSION ## TODO: should this mentioned above be e.g. the default value?

Value

Standardized fusion calls with aggregated Caller and read support

Examples

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# standardize
fusionfileArriba <- read_arriba_calls(
  system.file("extdata", "arriba_example.tsv", package = "annoFuseData")
)
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"
)
# merge standardized fusion calls
standardFusioncalls <- as.data.frame(rbind(formattedStarFusion, formattedArriba))
fusionQCFiltered <- fusion_filtering_QC(
  standardFusioncalls = standardFusioncalls,
  readingFrameFilter = "in-frame|frameshift|other",
  artifactFilter = "GTEx_Recurrent|DGD_PARALOGS|Normal|BodyMap|ConjoinG",
  junctionReadCountFilter = 1,
  spanningFragCountFilter = 10,
  readthroughFilter = TRUE
)
# aggregate calls
aggregate_fusion_calls(fusionQCFiltered)

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