context("Test fusion driver")
fusionfileArriba <- read_arriba_calls(system.file("extdata", "arriba_example.tsv", package = "annoFuseData"))
sfc <-
annoFuse::fusion_standardization(
fusion_calls = fusionfileArriba,
caller = "ARRIBA",
tumorID = "BS_W97QQYKQ"
)
geneListReferenceDataTab <- read.delim(system.file("extdata", "genelistreference.txt", package = "annoFuseData"), stringsAsFactors = FALSE)
fusionReferenceDataTab <- read.delim(system.file("extdata", "fusionreference.txt", package = "annoFuseData"), stringsAsFactors = FALSE)
bioMartDataPfam <- readRDS(system.file("extdata", "pfamDataBioMart.RDS", package = "annoFuseData"))
kinaseid <- unique(bioMartDataPfam$pfam_id[grep("kinase", bioMartDataPfam$NAME)])
fusion_driver_df <- fusion_driver(sfc,
annotated = FALSE,
geneListReferenceDataTab = geneListReferenceDataTab,
fusionReferenceDataTab = fusionReferenceDataTab,
checkDomainStatus = TRUE,
domainsToCheck = kinaseid
)
test_that("Fusion driver annotation for standardized arriba calls", {
expect_equal(colnames(fusion_driver_df), c("LeftBreakpoint", "RightBreakpoint", "FusionName", "Sample", "Caller", "Fusion_Type", "JunctionReadCount", "SpanningFragCount", "Confidence", "annots", "GeneA", "Gene1A", "Gene2A", "GeneB", "Gene1B", "Gene2B", "BreakpointLocation", "SpanningDelta", "DomainRetainedGene1A", "DomainRetainedGene1B", "reciprocal_exists", "Gene1A_anno", "Gene1B_anno", "Gene2A_anno", "Gene2B_anno", "Fusion_anno"))
expect_equal(nrow(fusion_driver_df), 5)
expect_equal(fusion_driver_df$DomainRetainedGene1B[1], "Yes")
})
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