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require(methods)
# S4 classes
setClass("DGEExact",
representation("list")
)
setClass("DGEList",
representation("list")
)
setClass("DGEGLM",
representation("list")
)
setClass("DGELRT",
representation("list")
)
setClass("TopTags",
representation("list")
)
# Set inheritance
# The LargeDataObject class is set in limma and provides a show method
setIs("DGEList","LargeDataObject")
setIs("DGEExact","LargeDataObject")
setIs("DGEGLM","LargeDataObject")
setIs("DGELRT","LargeDataObject")
# Show method
setMethod("show", "TopTags", function(object) {
if(object$test=="exact") {
cat("Comparison of groups: ",paste(rev(object$comparison),collapse="-"),"\n")
} else {
cat("Coefficient: ",object$comparison,"\n")
}
print(object$table)
})
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