tests/testthat/test_robust.R
In lgatto/MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics
context("Robust summarisation aggregation")
## This are the values calculated using data(msnset) and the orginal
## code provided by Adriaan Sticker, prior to refactoring to include
## into MSnbase. These data have been produced after removing X46 that
## contains one NA.
exp2 <- structure(c(885.188718025484, 17593.5475899093,
4923.62812560424, 1524.14767264389,
1069.94458515849, 1101.0620483011,
5852.6654376369, 760.032042354345,
6448.08286505193, 2278.3661184581,
32838.0439499617, 5135.5601051636,
21262.1475404352, 3715.08931949269,
4483.31990008056, 1147.0379543528,
26143.7541643903, 739.98608353734,
2770.37693640403, 2092.47630918864,
30047.2436312884, 11947.8807705827,
1259.1889827475, 4458.77171226405,
3824.35622986034, 2502.77917635441,
8635.31649124995, 3086.44980508555,
6670.69421123341, 31892.8927857503,
8504.48166594654, 2800.39559176937,
7540.63725898787, 1098.20952160703,
27638.3581933826, 1566.74773280695,
722.298177056015, 10154.9532804489,
11673.5920226627, 38262.1780306886,
1794.1744584286, 18545.6197157167,
5557.81802197453, 1399.89688059501,
1035.68883815967, 1124.16708243825,
5964.39464343898, 866.440367104486,
6234.19567901641, 2570.08000953496,
37066.0577703491, 5519.05329268798,
23168.7291266322, 4254.32256129384,
4873.99605610222, 1281.25856410339,
29677.4781315885, 799.350124068558,
2907.22208145075, 1993.87953759916,
31498.2176392823, 13061.8749812692,
1448.3734087348, 4786.51826088317,
3746.26739286631, 3013.04268418811,
10036.5290785991, 3266.41942225583,
7141.72540647816, 33634.69800926,
9924.07051063143, 3244.97753785551,
7679.15758221596, 984.645112269558,
33394.0252374262, 1444.27953283116,
1058.87115819752, 10486.9426673427,
11936.426138571, 32907.0889929717,
3157.01358505773, 19361.8367030621,
5775.20250520669, 1547.2184817791,
1029.41993487254, 1140.0931108892,
5970.36942510493, 883.909954763949,
6902.8902874887, 2785.56561793108,
41429.6267058477, 5828.37084272504,
25407.0684720129, 4748.46151560312,
6743.44063210487, 1278.70097099617,
29089.0593050867, 712.59829556942,
3055.51652965136, 2371.34243719932,
38489.8088214397, 12809.491407752,
1653.74895876646, 4350.78472106531,
4285.02115055174, 3017.53818337992,
9254.43168258667, 4093.80327095091,
7091.15089240577, 37674.727212131,
10058.2659687344, 2965.31877342984,
7561.98333513737, 1236.19285256579,
32104.2878604829, 1455.8965883255,
851.470159143209, 11018.1911818683,
12090.9319498833, 15000.1110553568,
7098.84112878367, 18328.2365038097,
5079.2951790709, 1563.22990202904,
999.695685420185, 1191.80548018217,
6006.8593209032, 791.329627946019,
6437.23029309139, 2446.79895107448,
39700.4751771986, 5583.72953182459,
25949.9540396184, 5249.90356134251,
4601.37757816911, 1175.08044352382,
27902.5607625172, 940.679303489625,
2946.79965814017, 2620.85662680864,
38275.2637470067, 12911.4785282575,
1261.52449379861, 4303.02562886477,
3649.44421585836, 2996.31272624433,
7769.74907445163, 3905.62405605242,
6779.99942643754, 37227.711932838,
9611.86445650645, 3184.19385924935,
8005.17654272541, 1173.12220480572,
26628.7277633697, 1557.19896062836,
944.628683254123, 11289.5520156138,
12268.6965850203, 10733.3352748144),
.Dim = c(40L, 4L),
.Dimnames = list(c("BSA", "ECA0172", "ECA0435",
"ECA0452", "ECA0469", "ECA0621",
"ECA0631", "ECA0691", "ECA0871",
"ECA0978", "ECA1032", "ECA1093",
"ECA1104", "ECA1294", "ECA1362",
"ECA1363", "ECA1364", "ECA1422",
"ECA1443", "ECA2186", "ECA2391",
"ECA2421", "ECA2831", "ECA3082",
"ECA3175", "ECA3349", "ECA3356",
"ECA3377", "ECA3566", "ECA3882",
"ECA3929", "ECA3969", "ECA4013",
"ECA4026", "ECA4030", "ECA4037",
"ECA4512", "ECA4513", "ECA4514",
"ENO"),
c("iTRAQ4.114", "iTRAQ4.115",
"iTRAQ4.116", "iTRAQ4.117")))
## These have been created when only the single NA is removed
exp1 <- structure(c(885.188718025484, 17593.5475899093,
4923.62812560424, 1524.14767264389,
1069.94458515849, 1101.0620483011,
5852.6654376369, 760.032042354345,
6448.08286505193, 2278.3661184581,
32838.0439499617, 5135.5601051636,
21262.1475404352, 3715.08931949269,
4483.31990008056, 1147.0379543528,
26143.7541643903, 739.98608353734,
2770.37693640403, 2092.47630918864,
30047.2436312884, 11947.8807705827,
1259.1889827475, 4458.77171226405,
3824.35622986034, 2502.77917635441,
8635.31649124995, 3086.44980508555,
6670.69421123341, 31892.8927857503,
8504.48166594654, 2800.39559176937,
7540.63725898787, 1098.20952160703,
27638.3581933826, 1566.74773280695,
722.298177056015, 10154.9532804489,
11673.5920226627, 22671.7355697837,
1794.1744584286, 18545.6197157167,
5557.81802197453, 1399.89688059501,
1035.68883815967, 1124.16708243825,
5964.39464343898, 866.440367104486,
6234.19567901641, 2570.08000953496,
37066.0577703491, 5519.05329268798,
23168.7291266322, 4254.32256129384,
4873.99605610222, 1281.25856410339,
29677.4781315885, 799.350124068558,
2907.22208145075, 1993.87953759916,
31498.2176392823, 13061.8749812692,
1448.3734087348, 4786.51826088317,
3746.26739286631, 3013.04268418811,
10036.5290785991, 3266.41942225583,
7141.72540647816, 33634.69800926,
9924.07051063143, 3244.97753785551,
7679.15758221596, 984.645112269558,
33394.0252374262, 1444.27953283116,
1058.87115819752, 10486.9426673427,
11936.426138571, 19986.1636445553,
3157.01358505773, 19361.8367030621,
5775.20250520669, 1547.2184817791,
1029.41993487254, 1140.0931108892,
5970.36942510493, 883.909954763949,
6902.8902874887, 2785.56561793108,
41429.6267058477, 5828.37084272504,
25407.0684720129, 4748.46151560312,
6743.44063210487, 1278.70097099617,
29089.0593050867, 712.59829556942,
3055.51652965136, 2371.34243719932,
38489.8088214397, 12809.491407752,
1653.74895876646, 4350.78472106531,
4285.02115055174, 3017.53818337992,
9254.43168258667, 4093.80327095091,
7091.15089240577, 37674.727212131,
10058.2659687344, 2965.31877342984,
7561.98333513737, 1236.19285256579,
32104.2878604829, 1455.8965883255,
851.470159143209, 11018.1911818683,
12090.9319498833, 16679.5719334398,
7098.84112878367, 18328.2365038097,
5079.2951790709, 1563.22990202904,
999.695685420185, 1191.80548018217,
6006.8593209032, 791.329627946019,
6437.23029309139, 2446.79895107448,
39700.4751771986, 5583.72953182459,
25949.9540396184, 5249.90356134251,
4601.37757816911, 1175.08044352382,
27902.5607625172, 940.679303489625,
2946.79965814017, 2620.85662680864,
38275.2637470067, 12911.4785282575,
1261.52449379861, 4303.02562886477,
3649.44421585836, 2996.31272624433,
7769.74907445163, 3905.62405605242,
6779.99942643754, 37227.711932838,
9611.86445650645, 3184.19385924935,
8005.17654272541, 1173.12220480572,
26628.7277633697, 1557.19896062836,
944.628683254123, 11289.5520156138,
12268.6965850203, 16885.1437447593),
.Dim = c(40L, 4L),
.Dimnames = list(c("BSA", "ECA0172", "ECA0435",
"ECA0452", "ECA0469", "ECA0621",
"ECA0631", "ECA0691", "ECA0871",
"ECA0978", "ECA1032", "ECA1093",
"ECA1104", "ECA1294", "ECA1362",
"ECA1363", "ECA1364", "ECA1422",
"ECA1443", "ECA2186", "ECA2391",
"ECA2421", "ECA2831", "ECA3082",
"ECA3175", "ECA3349", "ECA3356",
"ECA3377", "ECA3566", "ECA3882",
"ECA3929", "ECA3969", "ECA4013",
"ECA4026", "ECA4030", "ECA4037",
"ECA4512", "ECA4513", "ECA4514",
"ENO"),
c("iTRAQ4.114", "iTRAQ4.115",
"iTRAQ4.116", "iTRAQ4.117")))
test_that("Robust summarisation", {
data("msnset")
## Single NA value is removed prior to fit
expect_message(res1 <- combineFeatures(msnset,
fcol = "ProteinAccession",
method = "robust",
maxit = 100L))
expect_equal(exp1, exprs(res1))
## remove feature with missing value
msnset <- filterNA(msnset)
res2 <- combineFeatures(msnset,
fcol = "ProteinAccession",
method = "robust",
maxit = 100L)
expect_equal(exp2, exprs(res2))
notENO <- featureNames(res1) != "ENO"
expect_equal(exprs(res1)[notENO, ], exprs(res2)[notENO, ])
## all false (0)
expect_identical(sum(exprs(res1)[!notENO, ] == exprs(res2)[!notENO, ]), 0L)
})
lgatto/MSnbase documentation built on March 14, 2024, 7:06 a.m.
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context("Robust summarisation aggregation")
## This are the values calculated using data(msnset) and the orginal
## code provided by Adriaan Sticker, prior to refactoring to include
## into MSnbase. These data have been produced after removing X46 that
## contains one NA.
exp2 <- structure(c(885.188718025484, 17593.5475899093,
4923.62812560424, 1524.14767264389,
1069.94458515849, 1101.0620483011,
5852.6654376369, 760.032042354345,
6448.08286505193, 2278.3661184581,
32838.0439499617, 5135.5601051636,
21262.1475404352, 3715.08931949269,
4483.31990008056, 1147.0379543528,
26143.7541643903, 739.98608353734,
2770.37693640403, 2092.47630918864,
30047.2436312884, 11947.8807705827,
1259.1889827475, 4458.77171226405,
3824.35622986034, 2502.77917635441,
8635.31649124995, 3086.44980508555,
6670.69421123341, 31892.8927857503,
8504.48166594654, 2800.39559176937,
7540.63725898787, 1098.20952160703,
27638.3581933826, 1566.74773280695,
722.298177056015, 10154.9532804489,
11673.5920226627, 38262.1780306886,
1794.1744584286, 18545.6197157167,
5557.81802197453, 1399.89688059501,
1035.68883815967, 1124.16708243825,
5964.39464343898, 866.440367104486,
6234.19567901641, 2570.08000953496,
37066.0577703491, 5519.05329268798,
23168.7291266322, 4254.32256129384,
4873.99605610222, 1281.25856410339,
29677.4781315885, 799.350124068558,
2907.22208145075, 1993.87953759916,
31498.2176392823, 13061.8749812692,
1448.3734087348, 4786.51826088317,
3746.26739286631, 3013.04268418811,
10036.5290785991, 3266.41942225583,
7141.72540647816, 33634.69800926,
9924.07051063143, 3244.97753785551,
7679.15758221596, 984.645112269558,
33394.0252374262, 1444.27953283116,
1058.87115819752, 10486.9426673427,
11936.426138571, 32907.0889929717,
3157.01358505773, 19361.8367030621,
5775.20250520669, 1547.2184817791,
1029.41993487254, 1140.0931108892,
5970.36942510493, 883.909954763949,
6902.8902874887, 2785.56561793108,
41429.6267058477, 5828.37084272504,
25407.0684720129, 4748.46151560312,
6743.44063210487, 1278.70097099617,
29089.0593050867, 712.59829556942,
3055.51652965136, 2371.34243719932,
38489.8088214397, 12809.491407752,
1653.74895876646, 4350.78472106531,
4285.02115055174, 3017.53818337992,
9254.43168258667, 4093.80327095091,
7091.15089240577, 37674.727212131,
10058.2659687344, 2965.31877342984,
7561.98333513737, 1236.19285256579,
32104.2878604829, 1455.8965883255,
851.470159143209, 11018.1911818683,
12090.9319498833, 15000.1110553568,
7098.84112878367, 18328.2365038097,
5079.2951790709, 1563.22990202904,
999.695685420185, 1191.80548018217,
6006.8593209032, 791.329627946019,
6437.23029309139, 2446.79895107448,
39700.4751771986, 5583.72953182459,
25949.9540396184, 5249.90356134251,
4601.37757816911, 1175.08044352382,
27902.5607625172, 940.679303489625,
2946.79965814017, 2620.85662680864,
38275.2637470067, 12911.4785282575,
1261.52449379861, 4303.02562886477,
3649.44421585836, 2996.31272624433,
7769.74907445163, 3905.62405605242,
6779.99942643754, 37227.711932838,
9611.86445650645, 3184.19385924935,
8005.17654272541, 1173.12220480572,
26628.7277633697, 1557.19896062836,
944.628683254123, 11289.5520156138,
12268.6965850203, 10733.3352748144),
.Dim = c(40L, 4L),
.Dimnames = list(c("BSA", "ECA0172", "ECA0435",
"ECA0452", "ECA0469", "ECA0621",
"ECA0631", "ECA0691", "ECA0871",
"ECA0978", "ECA1032", "ECA1093",
"ECA1104", "ECA1294", "ECA1362",
"ECA1363", "ECA1364", "ECA1422",
"ECA1443", "ECA2186", "ECA2391",
"ECA2421", "ECA2831", "ECA3082",
"ECA3175", "ECA3349", "ECA3356",
"ECA3377", "ECA3566", "ECA3882",
"ECA3929", "ECA3969", "ECA4013",
"ECA4026", "ECA4030", "ECA4037",
"ECA4512", "ECA4513", "ECA4514",
"ENO"),
c("iTRAQ4.114", "iTRAQ4.115",
"iTRAQ4.116", "iTRAQ4.117")))
## These have been created when only the single NA is removed
exp1 <- structure(c(885.188718025484, 17593.5475899093,
4923.62812560424, 1524.14767264389,
1069.94458515849, 1101.0620483011,
5852.6654376369, 760.032042354345,
6448.08286505193, 2278.3661184581,
32838.0439499617, 5135.5601051636,
21262.1475404352, 3715.08931949269,
4483.31990008056, 1147.0379543528,
26143.7541643903, 739.98608353734,
2770.37693640403, 2092.47630918864,
30047.2436312884, 11947.8807705827,
1259.1889827475, 4458.77171226405,
3824.35622986034, 2502.77917635441,
8635.31649124995, 3086.44980508555,
6670.69421123341, 31892.8927857503,
8504.48166594654, 2800.39559176937,
7540.63725898787, 1098.20952160703,
27638.3581933826, 1566.74773280695,
722.298177056015, 10154.9532804489,
11673.5920226627, 22671.7355697837,
1794.1744584286, 18545.6197157167,
5557.81802197453, 1399.89688059501,
1035.68883815967, 1124.16708243825,
5964.39464343898, 866.440367104486,
6234.19567901641, 2570.08000953496,
37066.0577703491, 5519.05329268798,
23168.7291266322, 4254.32256129384,
4873.99605610222, 1281.25856410339,
29677.4781315885, 799.350124068558,
2907.22208145075, 1993.87953759916,
31498.2176392823, 13061.8749812692,
1448.3734087348, 4786.51826088317,
3746.26739286631, 3013.04268418811,
10036.5290785991, 3266.41942225583,
7141.72540647816, 33634.69800926,
9924.07051063143, 3244.97753785551,
7679.15758221596, 984.645112269558,
33394.0252374262, 1444.27953283116,
1058.87115819752, 10486.9426673427,
11936.426138571, 19986.1636445553,
3157.01358505773, 19361.8367030621,
5775.20250520669, 1547.2184817791,
1029.41993487254, 1140.0931108892,
5970.36942510493, 883.909954763949,
6902.8902874887, 2785.56561793108,
41429.6267058477, 5828.37084272504,
25407.0684720129, 4748.46151560312,
6743.44063210487, 1278.70097099617,
29089.0593050867, 712.59829556942,
3055.51652965136, 2371.34243719932,
38489.8088214397, 12809.491407752,
1653.74895876646, 4350.78472106531,
4285.02115055174, 3017.53818337992,
9254.43168258667, 4093.80327095091,
7091.15089240577, 37674.727212131,
10058.2659687344, 2965.31877342984,
7561.98333513737, 1236.19285256579,
32104.2878604829, 1455.8965883255,
851.470159143209, 11018.1911818683,
12090.9319498833, 16679.5719334398,
7098.84112878367, 18328.2365038097,
5079.2951790709, 1563.22990202904,
999.695685420185, 1191.80548018217,
6006.8593209032, 791.329627946019,
6437.23029309139, 2446.79895107448,
39700.4751771986, 5583.72953182459,
25949.9540396184, 5249.90356134251,
4601.37757816911, 1175.08044352382,
27902.5607625172, 940.679303489625,
2946.79965814017, 2620.85662680864,
38275.2637470067, 12911.4785282575,
1261.52449379861, 4303.02562886477,
3649.44421585836, 2996.31272624433,
7769.74907445163, 3905.62405605242,
6779.99942643754, 37227.711932838,
9611.86445650645, 3184.19385924935,
8005.17654272541, 1173.12220480572,
26628.7277633697, 1557.19896062836,
944.628683254123, 11289.5520156138,
12268.6965850203, 16885.1437447593),
.Dim = c(40L, 4L),
.Dimnames = list(c("BSA", "ECA0172", "ECA0435",
"ECA0452", "ECA0469", "ECA0621",
"ECA0631", "ECA0691", "ECA0871",
"ECA0978", "ECA1032", "ECA1093",
"ECA1104", "ECA1294", "ECA1362",
"ECA1363", "ECA1364", "ECA1422",
"ECA1443", "ECA2186", "ECA2391",
"ECA2421", "ECA2831", "ECA3082",
"ECA3175", "ECA3349", "ECA3356",
"ECA3377", "ECA3566", "ECA3882",
"ECA3929", "ECA3969", "ECA4013",
"ECA4026", "ECA4030", "ECA4037",
"ECA4512", "ECA4513", "ECA4514",
"ENO"),
c("iTRAQ4.114", "iTRAQ4.115",
"iTRAQ4.116", "iTRAQ4.117")))
test_that("Robust summarisation", {
data("msnset")
## Single NA value is removed prior to fit
expect_message(res1 <- combineFeatures(msnset,
fcol = "ProteinAccession",
method = "robust",
maxit = 100L))
expect_equal(exp1, exprs(res1))
## remove feature with missing value
msnset <- filterNA(msnset)
res2 <- combineFeatures(msnset,
fcol = "ProteinAccession",
method = "robust",
maxit = 100L)
expect_equal(exp2, exprs(res2))
notENO <- featureNames(res1) != "ENO"
expect_equal(exprs(res1)[notENO, ], exprs(res2)[notENO, ])
## all false (0)
expect_identical(sum(exprs(res1)[!notENO, ] == exprs(res2)[!notENO, ]), 0L)
})
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