tests/testthat/test_Proteins-functions.R

In Pbase: Manipulating and exploring protein and proteomics data

context("Proteins-functions")

## test_that("proteinCoverage", {
##     # build fake Proteins
##     p <- Proteins()
##     p@aa <- AAStringSet(c(P1="ABCDEF", P2="ABCD", P3="HIJKL"))
##     mcols(p@aa)$Ranges <- IRangesList(P1=IRanges(1, 6), P2=IRanges(1, 3), P3=IRanges())
##     mcols(p@aa) <- DataFrame(AccessionNumber=c("P1", "P2", "P3"))   
##     expect_equal(acols(proteinCoverage(p))$Coverage, c(P1=1, P2=0.75, P3=0))  
## })

test_that("rmEmptyRanges", {
    p <- Proteins()
    p@aa <- AAStringSet(c(P1="ABCDEF", P2="ABCD", P3="HIJKL"))
    mcols(p@aa)$Ranges <- IRangesList(P1=IRanges(1, 6), P2=IRanges(1, 3), P3=IRanges())
    pr <- Proteins()
    pr@aa <- AAStringSet(c(P1="ABCDEF", P2="ABCD"))
    mcols(pr@aa)$Ranges <- IRangesList(P1=IRanges(1, 6), P2=IRanges(1, 3))
    pr@metadata <- p@metadata    
    expect_equal(rmEmptyRanges(p), pr)
})