View source: R/fusion_filtering_QC.R
fusion_filtering_QC | R Documentation |
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
fusion_filtering_QC( standardFusioncalls, readingFrameFilter = "in-frame|frameshift|other", artifactFilter, junctionReadCountFilter, spanningFragCountFilter = 100, readthroughFilter = TRUE )
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 |
Standardized fusion calls filtered to pass QC and remove calls with insufficient read-support and annotation red-flags
# 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 )
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.