fusion_filtering_QC: Filters standardized fusion calls to remove artifacts and...

Description Usage Arguments Value Examples

View source: R/fusion_filtering_QC.R

Description

Events such as polymerase read-throughs, mis-mapping due to gene homology, and fusions occurring in healthy normal tissue require stringent filtering, making it difficult for researchers and clinicians to discern true underlying oncogenic drivers of a tumor and in some cases, appropriate therapy

Usage

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fusion_filtering_QC(
  standardFusioncalls,
  readingFrameFilter = "in-frame|frameshift|other",
  artifactFilter,
  junctionReadCountFilter,
  spanningFragCountFilter = 100,
  readthroughFilter = TRUE
)

Arguments

standardFusioncalls

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

readingFrameFilter

A regex to capture readingframe (eg. in-frame|frameshift|other)

artifactFilter

A red flag filter from Annotation ; in OpenPBTA annotation is from FusionAnnotator column "annots"

junctionReadCountFilter

An integer threshold for JunctionReadCount

spanningFragCountFilter

An integer threshold for (SpanningFragCount - JunctionReadCount)

readthroughFilter

Boolean for filtering readthroughs

Value

Standardized fusion calls filtered to pass QC and remove calls with insufficient read-support and annotation red-flags

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 = 100,
  readthroughFilter = TRUE
)

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