View source: R/annoFuse_single_sample.R
annoFuse_single_sample | R Documentation |
Performs artifact filter to remove readthroughs,red flags and performs expression filtering with user provided expression Matrix and expression threshold
annoFuse_single_sample( fusionfileArriba, fusionfileStarFusion, expressionFile = NULL, expressionFilter = 1, tumorID = "tumorID", readingFrameFilter = "in-frame|frameshift|other", readthroughFilter = FALSE, artifactFilter = "GTEx_Recurrent|DGD_PARALOGS|Normal|BodyMap|ConjoinG", junctionReadCountFilter = 1, spanningFragCountFilter = 10 )
fusionfileArriba |
A dataframe from arriba fusion caller |
fusionfileStarFusion |
A dataframe from starfusion caller |
expressionFile |
Expression matrix for samples used in cohort for fusion calls |
expressionFilter |
FPKM/TPM threshold for not expressed |
tumorID |
Sample name to be used |
readingFrameFilter |
A regex to capture readingframe (eg. in-frame|frameshift|other) |
readthroughFilter |
Boolean for filtering readthroughs |
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) |
Standardized fusion calls annotated with gene list and fusion list provided in reference folder
standardFusioncalls <- annoFuse::annoFuse_single_sample( # Example files are provided in extdata, at-least 1 fusionfile is required along # with its rsem expression file fusionfileArriba = system.file( "extdata", "arriba_example.tsv", package = "annoFuseData" ), fusionfileStarFusion = system.file( "extdata", "starfusion_example.tsv", package = "annoFuseData" ), expressionFile = system.file( "extdata", "example.rsem.genes.results.gz", package = "annoFuseData" ), tumorID = "BS_W97QQYKQ", # multiple read flag values for filtering using FusionAnnotator values artifactFilter = "GTEx_Recurrent|DGD_PARALOGS|Normal|BodyMap|ConjoinG", # keep all in-frame , frameshift and other types of Fusion_Type readingFrameFilter = "in-frame|frameshift|other", # keep all fusions with atleast 1 junction read support junctionReadCountFilter = 1, # keep only fusions where spanningFragCount-junctionReadCountFilter less than equal to 10 spanningFragCountFilter = 10, # keep read throughs readthroughFilter = FALSE )
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