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

In d3b-center/annoFuse: annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions

Function to aggregate Caller and read support per fusions calls

Description

Function to aggregate Caller and read support per fusions calls

Usage

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

# 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 Feb. 21, 2023, 1:06 a.m.