context("Metacell methods test") # require(DAPARdata) # data(Exp1_R2_pept) # obj <- Exp1_R2_pept[1:50] # test <- Exp1_R2_pept[130:140] # test2 <- Exp1_R2_pept[20:28] # # # test_that("getPourcentageOfMV", { # # expect_equal(round(getPourcentageOfMV(test), 2), 28.79) # }) # # # # # # test_that("getIndicesOfLinesToRemove", { # # expect_equal(getIndicesOfLinesToRemove(test2, "Potential.contaminant", prefix="+"), 9) # expect_equal(getIndicesOfLinesToRemove(test2, "Potential.contaminant"), NULL) # }) # # # # # test_that("getNumberOf", { # # expect_equal(getNumberOf(test2,"Potential.contaminant", "+"), 1) # expect_equal(getNumberOf(test2,"Potential.contaminant", "+abc"), 0) # expect_equal(getNumberOf(test2,"Potential.contaminant"), 0) # expect_equal(getNumberOf(test2, prefix="+"), 0) # expect_equal(getNumberOf(test2), 0) # }) # # # # test_that("removeLines", { # # Mout <- matrix(c(24.8037, 24.8458, 24.9518, 24.8411, 24.8445, 24.5173, # NA, 22.7895, 22.1014, NA, 23.1118, NA, # NA, NA, NA, NA, NA, NA, # 22.2452, NA, 21.8009, NA, NA, NA, # NA, 22.3721, NA, NA, NA, NA, # NA, NA, NA, NA, NA, 23.1516, # 24.4367, 24.5145, 24.2637, 24.7409, 24.6064, 24.7815, # 24.2771, 24.4007, 24.1365, 24.9600, 25.0521, 25.0964), # byrow=TRUE, ncol=6, # dimnames = list(c(19:26), # c("Intensity.D.R1", "Intensity.D.R2", "Intensity.D.R3", "Intensity.E.R1", "Intensity.E.R2", "Intensity.E.R3"))) # expect_equal(round(exprs(removeLines(test2,"Potential.contaminant", "+")),4), Mout) # # expect_equal(Biobase::exprs(removeLines(test2,"Potential.contaminant")), Biobase::exprs(test2)) # expect_equal(Biobase::fData(removeLines(test2,"Potential.contaminant")), Biobase::fData(test2)) # expect_equal(Biobase::pData(removeLines(test2,"Potential.contaminant")), Biobase::pData(test2)) # }) # # # # test_that("mvFilterFromIndices", { # # expect_equal(Biobase::exprs(mvFilterFromIndices(Exp1_R2_pept,c(1:100, 200:300), "reverse")), Biobase::exprs(Exp1_R2_pept[c(1:100, 200:300)])) # expect_equal(Biobase::fData(mvFilterFromIndices(Exp1_R2_pept,c(1:100, 200:300), "reverse")), Biobase::fData(Exp1_R2_pept[c(1:100, 200:300)])) # expect_equal(Biobase::pData(mvFilterFromIndices(Exp1_R2_pept,c(1:100, 200:300), "reverse")), Biobase::pData(Exp1_R2_pept[c(1:100, 200:300)])) # # expect_equal(Biobase::exprs(mvFilterFromIndices(Exp1_R2_pept,c(1:100, 200:300), "contaminants")), Biobase::exprs(Exp1_R2_pept[c(1:100, 200:300)])) # expect_equal(Biobase::fData(mvFilterFromIndices(Exp1_R2_pept,c(1:100, 200:300), "contaminants")), Biobase::fData(Exp1_R2_pept[c(1:100, 200:300)])) # expect_equal(Biobase::pData(mvFilterFromIndices(Exp1_R2_pept,c(1:100, 200:300), "contaminants")), Biobase::pData(Exp1_R2_pept[c(1:100, 200:300)])) # }) # # # # # test_that("mvFilterFromIndices", { # expect_equal(Biobase::exprs(deleteLinesFromIndices(Exp1_R2_pept,c(1:100, 200:300), "reverse")), Biobase::exprs(Exp1_R2_pept[-c(1:100, 200:300)])) # expect_equal(Biobase::fData(deleteLinesFromIndices(Exp1_R2_pept,c(1:100, 200:300), "reverse")), Biobase::fData(Exp1_R2_pept[-c(1:100, 200:300)])) # expect_equal(Biobase::pData(deleteLinesFromIndices(Exp1_R2_pept,c(1:100, 200:300), "reverse")), Biobase::pData(Exp1_R2_pept[-c(1:100, 200:300)])) # # expect_equal(Biobase::exprs(deleteLinesFromIndices(Exp1_R2_pept,c(1:100, 200:300), "contaminants")), Biobase::exprs(Exp1_R2_pept[-c(1:100, 200:300)])) # expect_equal(Biobase::fData(deleteLinesFromIndices(Exp1_R2_pept,c(1:100, 200:300), "contaminants")), Biobase::fData(Exp1_R2_pept[-c(1:100, 200:300)])) # expect_equal(Biobase::pData(deleteLinesFromIndices(Exp1_R2_pept,c(1:100, 200:300), "contaminants")), Biobase::pData(Exp1_R2_pept[-c(1:100, 200:300)])) # }) # # # # # test_that("mvFilterFromIndices", { # t <- c(1,2,4,5,7,11) # names(t) <- c(129, 130, 132, 133, 135, 139) # expect_equal(mvFilterGetIndices(test, "wholeMatrix", 6), t) # # }) # # # # # test_that("Missing values filter, whole Matrix, no NA lines", { # # Mout <- matrix(c(28.1944, 28.0756, 28.1724, 28.3253, 28.4246, 28.3782, # 24.4159, 24.4346, 24.4237, 24.3140, 24.5114, 24.5450, # 22.6008, 22.9028, NA, 22.8938, 23.0190, NA, # 27.7759, 27.6335, 27.6969, 27.9458, 28.0809, 28.0318, # 24.7701, 24.7433, 24.6523, 24.5939, 24.0654, 24.3660, # 19.6482, NA, 22.9006, 23.2119, 23.1454, 22.9676, # 26.7079, 26.6682, 26.7437, 27.4372, 27.4080, 27.4981, # 25.3562, NA, NA, NA, NA, NA, # NA, NA, NA, NA, NA, 22.4979, # 29.4798, 29.5120, 29.4984, 29.6032, 29.6513, 29.7486), # byrow=TRUE, ncol=6, # dimnames = list(c(129:135, 137:139), # c("Intensity.D.R1", "Intensity.D.R2", "Intensity.D.R3", "Intensity.E.R1", "Intensity.E.R2", "Intensity.E.R3"))) # # # expect_equal(round(Biobase::exprs(mvFilter(test, "wholeMatrix", th=as.integer(1))), 4), Mout) # expect_equal(round(Biobase::exprs(mvFilter(test, "wholeMatrix", th=1)), 4), Mout) # }) # # # test_that("Missing values filter, # at least 2 intensities for each condition", { # # Mout <- matrix(c(28.1944, 28.0756, 28.1724, 28.3253, 28.4246, 28.3782, # 24.4159, 24.4346, 24.4237, 24.3140, 24.5114, 24.5450, # 22.6008, 22.9028, NA, 22.8938, 23.0190, NA, # 27.7759, 27.6335, 27.6969, 27.9458, 28.0809, 28.0318, # 24.7701, 24.7433, 24.6523, 24.5939, 24.0654, 24.3660, # 19.6482, NA, 22.9006, 23.2119, 23.1454, 22.9676, # 26.7079, 26.6682, 26.7437, 27.4372, 27.4080, 27.4981, # 29.4798, 29.5120, 29.4984, 29.6032, 29.6513, 29.7486), # byrow=TRUE, ncol=6, # dimnames = list(c(129:135, 139), # c("Intensity.D.R1", "Intensity.D.R2", "Intensity.D.R3", "Intensity.E.R1", "Intensity.E.R2", "Intensity.E.R3"))) # # # expect_equal(round(Biobase::exprs(mvFilter(test, "allCond", th=as.integer(2))),4), Mout) # expect_equal(round(Biobase::exprs(mvFilter(test, "allCond", th=2)),4), Mout) # }) # # # # # # test_that("Missing values filter, # at least 2 intensities ine one condition", { # # Mout <- matrix(c(28.1944, 28.0756, 28.1724, 28.3253, 28.4246, 28.3782, # 24.4159, 24.4346, 24.4237, 24.3140, 24.5114, 24.5450, # 22.6008, 22.9028, NA, 22.8938, 23.0190, NA, # 27.7759, 27.6335, 27.6969, 27.9458, 28.0809, 28.0318, # 24.7701, 24.7433, 24.6523, 24.5939, 24.0654, 24.3660, # 19.6482, NA, 22.9006, 23.2119, 23.1454, 22.9676, # 26.7079, 26.6682, 26.7437, 27.4372, 27.4080, 27.4981, # 29.4798, 29.5120, 29.4984, 29.6032, 29.6513, 29.7486), # byrow=TRUE, ncol=6, # dimnames = list(c(129:135,139), # c("Intensity.D.R1", "Intensity.D.R2", "Intensity.D.R3", "Intensity.E.R1", "Intensity.E.R2", "Intensity.E.R3")) # ) # # expect_equal(round(Biobase::exprs(mvFilter(test, "atLeastOneCond", th=as.integer(2))), 4), Mout) # expect_equal(round(Biobase::exprs(mvFilter(test, "atLeastOneCond", th=2)), 4), Mout) # })