View source: R/zscored_annotation.R
zscored_annotation | R Documentation |
The input should have the following standardized columns to run through this GTEx/cohort normalization function "Sample" Unique SampleIDs used in your RNAseq dataset "FusionName" GeneA–GeneB ,or if fusion is intergenic then Gene1A/Gene2A–GeneB
zscored_annotation( standardFusioncalls, zscoreFilter, saveZscoredMatrix, normData, expressionMatrix )
standardFusioncalls |
Annotates standardizes fusion calls from callers STARfusion| Arriba or QC filtered fusion |
zscoreFilter |
Zscore value to use as threshold for annotation of differential expression |
saveZscoredMatrix |
File to save zscored matrix calculated for the normalized data and expression matrix |
normData |
normalizing expression dataset to calculate zscore |
expressionMatrix |
Expression matrix associated with the fusion calls |
expression_annotated_fusions is a standardized fusion call set with standard
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 ) expressionMatrix <- readRDS(system.file("extdata", "expr_collapsed.rds", package = "annoFuseData")) normData <- readRDS(system.file("extdata", "gtex_collapsed.rds", package = "annoFuseData")) zscoredStandardFusioncalls <- zscored_annotation(standardFusioncalls, zscoreFilter = 2, normData = normData, expressionMatrix = expressionMatrix )
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