View source: R/annotate_fusion_calls.R
annotate_fusion_calls | R Documentation |
Function to annotate fusion calls
annotate_fusion_calls( standardFusioncalls, geneListReferenceDataTab, fusionReferenceDataTab, checkReciprocal = TRUE )
standardFusioncalls |
A dataframe from star fusion or arriba standardized to run through the filtering steps |
geneListReferenceDataTab |
A dataframe with column 1 as GeneName 2 source file 3 type; collapse to summarize type |
fusionReferenceDataTab |
A dataframe with column 1 as FusionName 2 source file 3 type; collapse to summarize type |
checkReciprocal |
Logical value to check if fusion also has reciprocal fusion in Sample, default to TRUE |
Standardized fusion calls annotated with gene list and fusion list provided in reference folder. If checkReciprocal ==TRUE reciprocal status of fusion is also provided .
# 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 ) # annotated from gene and fusion refrence list # read in gene and fusion reference tab geneListReferenceDataTab <- read.delim( system.file("extdata", "genelistreference.txt", package = "annoFuseData"), stringsAsFactors = FALSE ) # column 1 as FusionName 2 source file 3 type; collapse to summarize type fusionReferenceDataTab <- read.delim( system.file("extdata", "fusionreference.txt", package = "annoFuseData"), stringsAsFactors = FALSE ) filteredFusionAnnotated <- annotate_fusion_calls( standardFusioncalls = fusionQCFiltered, geneListReferenceDataTab = geneListReferenceDataTab, fusionReferenceDataTab = fusionReferenceDataTab, checkReciprocal = TRUE )
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