This function performs the split-apply-combine methodology on Phylostrata or Divergence Strata stored within the input PhyloExpressionSet.
This function is very useful to perform any phylostratum or divergence-stratum specific analysis.
Value
Either a numeric matrix storing the return values of the applied function for each age class or a numeric list storing the return values of the applied function for each age class in a list.
Details
This function uses the split function to subset the expression matrix into
phylostratum specific sub-matrices. Internally using lapply, any function can
be performed to the sub-matrices. The return value of this function is a numeric matrix storing
the return values by FUN for each phylostratum and each developmental stage s.
Note that the input FUN must be an function that can be applied to a matrix (e.g., colMeans).
In case you use an anonymous function you could use function(x) apply(x , 2 , var) as an example to compute the variance of each phylostratum and each
developmental stage s.
Examples
# source the example dataset
data(example_phyex_set)
# Example 1
# get the relative expression profiles for each phylostratum
age.apply(example_phyex_set, relative_expression)
#> Preglobular Globular Early Heart Late Heart
#> Cellular Organisms 2.605911e-01 0.12793981 0.000000000 0.026881705
#> Eukaryota 1.000000e+00 0.55293348 0.189559124 0.196201915
#> Viridiplantae 9.487069e-01 0.64837547 0.383978993 0.429882908
#> Streptophyta 4.841418e-01 0.32916458 0.135164508 0.268663521
#> Streptophytina 4.658941e-01 0.23957101 0.000000000 0.121559172
#> Embryophyta 1.000000e+00 0.66912196 0.128931740 0.000000000
#> Traceophyta 9.801590e-02 0.06042883 0.135543409 0.378021395
#> Euphyllophyta 0.000000e+00 0.04677271 0.087985328 0.168200972
#> Spermatophyta 7.810519e-01 0.58144016 0.223285879 0.337486796
#> Magnoliopsida 1.629285e-01 0.09061350 0.000000000 0.018285123
#> Mesangiospermae 4.038082e-02 0.01121083 0.000000000 0.005737602
#> Pentapetalae 3.246299e-01 0.21700156 0.144509595 0.097944252
#> Rosids 3.326239e-01 0.11927725 0.032900891 0.027334952
#> Malvids 9.283219e-05 0.00000000 0.002602139 0.010052870
#> Brassicales 5.345106e-02 0.01215026 0.000000000 0.007310340
#> Brassicaceae 1.000000e+00 0.60384609 0.241587219 0.110540287
#> Camelineae 1.000000e+00 0.33199892 0.344002183 0.000000000
#> Arabidopsis 9.861585e-01 0.16623807 0.055818498 0.000000000
#> Arabidopsis thaliana 4.013569e-01 0.15321763 0.000000000 0.116830157
#> Early Torpedo Late Torpedo Bent Cotyledon Mature Green
#> Cellular Organisms 0.20663298 0.21843800 0.097548168 1.0000000
#> Eukaryota 0.69151453 0.57874362 0.000000000 0.4467661
#> Viridiplantae 1.00000000 0.97389494 0.179728213 0.0000000
#> Streptophyta 0.94067019 1.00000000 0.000000000 0.6574747
#> Streptophytina 1.00000000 0.92977692 0.022839379 0.6142885
#> Embryophyta 0.32543544 0.12254727 0.132335580 0.5435090
#> Traceophyta 0.95513332 1.00000000 0.530095060 0.0000000
#> Euphyllophyta 0.41611064 0.64059690 0.608733049 1.0000000
#> Spermatophyta 1.00000000 0.93870781 0.000000000 0.8373587
#> Magnoliopsida 0.24116992 0.24928704 0.206324828 1.0000000
#> Mesangiospermae 0.03784404 0.03927685 0.005984007 1.0000000
#> Pentapetalae 0.11205103 0.06150410 0.000000000 1.0000000
#> Rosids 0.06003207 0.03575030 0.000000000 1.0000000
#> Malvids 0.11014167 0.08366978 0.198889083 1.0000000
#> Brassicales 0.04177697 0.05724916 0.087448340 1.0000000
#> Brassicaceae 0.21256956 0.09035905 0.000000000 0.3169490
#> Camelineae 0.61326644 0.28343817 0.061167981 0.6789578
#> Arabidopsis 0.28692584 0.14326831 0.156220962 1.0000000
#> Arabidopsis thaliana 0.39498925 0.36292280 0.314706027 1.0000000
# this is analogous to
rel_exp_matrix(example_phyex_set)
#> Preglobular Globular Early Heart Late Heart Early Torpedo Late Torpedo
#> 1 2.605911e-01 0.12793981 0.000000000 0.026881705 0.20663298 0.21843800
#> 2 1.000000e+00 0.55293348 0.189559124 0.196201915 0.69151453 0.57874362
#> 3 9.487069e-01 0.64837547 0.383978993 0.429882908 1.00000000 0.97389494
#> 4 4.841418e-01 0.32916458 0.135164508 0.268663521 0.94067019 1.00000000
#> 5 4.658941e-01 0.23957101 0.000000000 0.121559172 1.00000000 0.92977692
#> 6 1.000000e+00 0.66912196 0.128931740 0.000000000 0.32543544 0.12254727
#> 7 9.801590e-02 0.06042883 0.135543409 0.378021395 0.95513332 1.00000000
#> 8 0.000000e+00 0.04677271 0.087985328 0.168200972 0.41611064 0.64059690
#> 9 7.810519e-01 0.58144016 0.223285879 0.337486796 1.00000000 0.93870781
#> 10 1.629285e-01 0.09061350 0.000000000 0.018285123 0.24116992 0.24928704
#> 11 4.038082e-02 0.01121083 0.000000000 0.005737602 0.03784404 0.03927685
#> 12 3.246299e-01 0.21700156 0.144509595 0.097944252 0.11205103 0.06150410
#> 13 3.326239e-01 0.11927725 0.032900891 0.027334952 0.06003207 0.03575030
#> 14 9.283219e-05 0.00000000 0.002602139 0.010052870 0.11014167 0.08366978
#> 15 5.345106e-02 0.01215026 0.000000000 0.007310340 0.04177697 0.05724916
#> 16 1.000000e+00 0.60384609 0.241587219 0.110540287 0.21256956 0.09035905
#> 17 1.000000e+00 0.33199892 0.344002183 0.000000000 0.61326644 0.28343817
#> 18 9.861585e-01 0.16623807 0.055818498 0.000000000 0.28692584 0.14326831
#> 19 4.013569e-01 0.15321763 0.000000000 0.116830157 0.39498925 0.36292280
#> Bent Cotyledon Mature Green
#> 1 0.097548168 1.0000000
#> 2 0.000000000 0.4467661
#> 3 0.179728213 0.0000000
#> 4 0.000000000 0.6574747
#> 5 0.022839379 0.6142885
#> 6 0.132335580 0.5435090
#> 7 0.530095060 0.0000000
#> 8 0.608733049 1.0000000
#> 9 0.000000000 0.8373587
#> 10 0.206324828 1.0000000
#> 11 0.005984007 1.0000000
#> 12 0.000000000 1.0000000
#> 13 0.000000000 1.0000000
#> 14 0.198889083 1.0000000
#> 15 0.087448340 1.0000000
#> 16 0.000000000 0.3169490
#> 17 0.061167981 0.6789578
#> 18 0.156220962 1.0000000
#> 19 0.314706027 1.0000000
# Example 2
# compute the mean expression profiles for each phylostratum
age.apply(example_phyex_set, colMeans)
#> Preglobular Globular Early Heart Late Heart
#> Cellular Organisms 319.2256868 257.52020702 198.006382 210.51096
#> Eukaryota 140.9937811 114.14220354 92.317321 92.71630
#> Viridiplantae 167.2580207 137.35667928 111.033065 115.60331
#> Streptophyta 91.2879207 84.80962271 76.700108 82.28058
#> Streptophytina 121.2804565 108.09604554 94.139882 101.22129
#> Embryophyta 345.0889115 296.06388693 216.025821 196.92246
#> Traceophyta 111.0771983 92.59719465 129.527919 248.74430
#> Euphyllophyta 352.3710864 386.91405362 417.350739 476.59226
#> Spermatophyta 110.5848040 102.51114553 88.024950 92.64401
#> Magnoliopsida 85.7850927 77.24344506 66.540425 68.70021
#> Mesangiospermae 103.8641965 78.17351420 68.299874 73.35311
#> Pentapetalae 151.8902778 117.40807204 94.182927 79.26421
#> Rosids 138.7250813 62.58309299 31.755946 29.76950
#> Malvids 0.1975973 0.06982345 3.651396 13.90655
#> Brassicales 350.8078278 203.10827402 159.656636 185.79981
#> Brassicaceae 1240.8340834 830.33617517 454.960581 319.16868
#> Camelineae 501.9910183 287.23392235 291.092877 180.49888
#> Arabidopsis 236.1796142 126.12962280 111.309071 103.81709
#> Arabidopsis thaliana 79.2626235 60.87854425 49.526997 58.18268
#> Early Torpedo Late Torpedo Bent Cotyledon Mature Green
#> Cellular Organisms 294.12595 299.61730 243.38291 663.17689
#> Eukaryota 122.46562 115.69240 80.93208 107.76561
#> Viridiplantae 172.36482 169.76577 90.69763 72.80368
#> Streptophyta 110.37154 112.85162 71.05001 98.53351
#> Streptophytina 152.39469 148.30386 95.47039 129.92514
#> Embryophyta 245.14108 215.07986 216.53016 277.45226
#> Traceophyta 532.48631 554.54540 323.51261 62.88684
#> Euphyllophyta 659.68056 825.47001 801.93765 1090.89936
#> Spermatophyta 119.44055 116.96148 78.99375 112.86223
#> Magnoliopsida 95.02676 95.98553 90.91095 184.65770
#> Mesangiospermae 101.63000 102.89190 73.57013 949.02303
#> Pentapetalae 83.78378 67.58943 47.88460 368.26696
#> Rosids 41.43888 32.77288 20.01384 376.90719
#> Malvids 151.66834 115.23254 273.81990 1376.46550
#> Brassicales 309.05905 364.39056 472.38859 3735.84753
#> Brassicaceae 424.89225 298.25672 204.62594 533.05112
#> Camelineae 377.65922 271.62202 200.16390 398.77848
#> Arabidopsis 142.32838 123.04661 124.78512 238.03743
#> Arabidopsis thaliana 78.79086 76.41513 72.84285 123.61474
# Example 3
# compute the variance profiles for each phylostratum
age.apply(example_phyex_set, function(x) apply(x , 2 , var))
#> Preglobular Globular Early Heart Late Heart
#> Cellular Organisms 375769.502 213691.418 93456.6263 111376.489
#> Eukaryota 18957.667 9246.500 4881.1656 5275.564
#> Viridiplantae 19765.672 9955.686 5088.6714 5898.013
#> Streptophyta 8988.070 5289.605 2911.2031 4200.383
#> Streptophytina 14051.461 9938.314 5196.7120 5942.141
#> Embryophyta 1682940.617 865145.071 456717.0145 340113.846
#> Traceophyta 11741.175 6082.060 27027.1280 232242.024
#> Euphyllophyta 305880.389 397342.608 519645.4590 678605.730
#> Spermatophyta 7915.181 6101.064 3870.7790 3901.142
#> Magnoliopsida 5305.453 4352.801 3774.8536 4394.796
#> Mesangiospermae 7492.982 5565.843 6237.1524 12496.953
#> Pentapetalae 41129.591 23603.672 16333.7718 10152.252
#> Rosids 53859.055 5195.222 1230.0765 1446.926
#> Malvids NA NA NA NA
#> Brassicales 316537.394 88058.415 47820.5856 53928.058
#> Brassicaceae 14885810.615 9941830.931 2669040.4130 1089242.891
#> Camelineae 307467.949 53236.390 115819.8364 16224.737
#> Arabidopsis 76646.093 16854.057 12918.5441 10053.409
#> Arabidopsis thaliana 1126.399 1146.464 999.1358 1331.448
#> Early Torpedo Late Torpedo Bent Cotyledon Mature Green
#> Cellular Organisms 388410.149 472014.5965 397835.8529 63911898.395
#> Eukaryota 13465.408 15107.5394 11822.8106 152722.168
#> Viridiplantae 16364.920 19284.1470 5212.9363 3250.544
#> Streptophyta 12769.289 15878.6702 2984.0422 27031.826
#> Streptophytina 16402.149 13306.9785 5833.6976 29315.188
#> Embryophyta 412912.826 295668.0230 790522.8496 414144.210
#> Traceophyta 1364256.658 1559803.5400 506744.6395 4122.238
#> Euphyllophyta 1257597.946 2173425.2889 2266699.0105 4675378.101
#> Spermatophyta 6605.489 5854.6060 4676.2139 56952.986
#> Magnoliopsida 8062.390 8888.6519 5562.2734 51672.097
#> Mesangiospermae 30301.931 42528.5521 9445.6795 8819608.027
#> Pentapetalae 9174.203 4831.4157 867.6210 649519.677
#> Rosids 3161.268 1742.4209 261.2453 193249.936
#> Malvids NA NA NA NA
#> Brassicales 76336.441 145638.0550 275410.3640 41379294.447
#> Brassicaceae 1578566.326 369065.8774 100803.7193 1284948.737
#> Camelineae 144921.918 63440.1248 96206.7819 338162.950
#> Arabidopsis 20162.613 12372.7956 20081.3084 100005.445
#> Arabidopsis thaliana 1192.349 580.5684 2527.3283 21297.735
# Example 4
# compute the range for each phylostratum
# Note: in this case, the range() function returns 2 values for each phylostratum
# and each developmental stage, hence one should use the argument 'as.list = TRUE'
# to make sure that the results are returned properly
age.apply(example_phyex_set, function(x) apply(x , 2 , range), as.list = TRUE)
#> $`Cellular Organisms`
#> Preglobular Globular Early Heart Late Heart Early Torpedo Late Torpedo
#> [1,] 0.000 0.000 0.000 0.000 0.00 3.544692e-02
#> [2,] 5564.301 4519.245 2919.754 4556.479 14832.43 1.875515e+04
#> Bent Cotyledon Mature Green
#> [1,] 0.00 0.0
#> [2,] 15615.46 232540.6
#>
#> $Eukaryota
#> Preglobular Globular Early Heart Late Heart Early Torpedo
#> [1,] 0.0000 0.00668537 0.02359617 0.0000 0.0000
#> [2,] 892.8625 719.63352333 500.92871828 502.5445 836.5676
#> Late Torpedo Bent Cotyledon Mature Green
#> [1,] 1.913363e-02 0.000 0.000
#> [2,] 1.066288e+03 1076.485 5007.653
#>
#> $Viridiplantae
#> Preglobular Globular Early Heart Late Heart Early Torpedo Late Torpedo
#> [1,] 5.170611 10.58502 18.8333 26.27958 52.45156 48.44215
#> [2,] 543.351669 416.02187 290.4093 325.57187 508.29134 671.60642
#> Bent Cotyledon Mature Green
#> [1,] 19.67485 11.01641
#> [2,] 339.55379 230.36384
#>
#> $Streptophyta
#> Preglobular Globular Early Heart Late Heart Early Torpedo
#> [1,] 0.1112127 0.02726316 0.2400369 0.4643987 1.437311
#> [2,] 429.2365901 298.91980215 249.1829693 368.5563000 669.422226
#> Late Torpedo Bent Cotyledon Mature Green
#> [1,] 3.658204 20.90519 0.6574457
#> [2,] 766.647581 338.46027 742.8222730
#>
#> $Streptophytina
#> Preglobular Globular Early Heart Late Heart Early Torpedo
#> [1,] 0.06808085 0.01162535 8.607448 21.13225 24.16181
#> [2,] 592.75789921 455.82413441 281.509058 280.86175 455.68970
#> Late Torpedo Bent Cotyledon Mature Green
#> [1,] 35.45795 27.6913 5.139044
#> [2,] 444.17275 315.3078 848.215171
#>
#> $Embryophyta
#> Preglobular Globular Early Heart Late Heart Early Torpedo
#> [1,] 7.526608e-02 3.427276e-02 1.299371e-02 6.769752e-02 0.2958471
#> [2,] 9.981932e+03 6.858560e+03 5.181343e+03 4.485187e+03 4853.5604685
#> Late Torpedo Bent Cotyledon Mature Green
#> [1,] 0.1505351 3.776421 0.191978
#> [2,] 4100.7403444 6952.029473 3766.979231
#>
#> $Traceophyta
#> Preglobular Globular Early Heart Late Heart Early Torpedo Late Torpedo
#> [1,] 28.6467 33.54971 38.44432 40.84347 43.16473 48.1074
#> [2,] 342.2688 259.05460 489.39943 1338.92886 3176.31691 3384.2641
#> Bent Cotyledon Mature Green
#> [1,] 33.7693 0.6672493
#> [2,] 1937.1539 189.5959594
#>
#> $Euphyllophyta
#> Preglobular Globular Early Heart Late Heart Early Torpedo
#> [1,] 0.1068995 2.429332e-02 1.783572 25.50669 54.57407
#> [2,] 1323.0953155 1.491979e+03 1689.893350 1933.14094 2652.15309
#> Late Torpedo Bent Cotyledon Mature Green
#> [1,] 55.45201 26.89962 3.153947
#> [2,] 3453.34947 3489.60651 4949.764295
#>
#> $Spermatophyta
#> Preglobular Globular Early Heart Late Heart Early Torpedo
#> [1,] 0.01479277 0.05749413 0.2470909 0.08216436 0.4607543
#> [2,] 396.58922233 330.25820591 295.1633296 316.74962222 353.8924251
#> Late Torpedo Bent Cotyledon Mature Green
#> [1,] 1.425323 4.34375 1.667889
#> [2,] 361.639571 308.00956 1321.199400
#>
#> $Magnoliopsida
#> Preglobular Globular Early Heart Late Heart Early Torpedo Late Torpedo
#> [1,] 0.0000 0.0000 0.000 0.0000 0.01505505 0.1552744
#> [2,] 227.9104 208.5809 261.676 301.9089 416.19400915 398.7333107
#> Bent Cotyledon Mature Green
#> [1,] 2.935162 1.141558
#> [2,] 288.410357 923.185945
#>
#> $Mesangiospermae
#> Preglobular Globular Early Heart Late Heart Early Torpedo Late Torpedo
#> [1,] 0.1096234 0.0000 0.0000 0.09332517 0.5496438 1.451886
#> [2,] 292.5547037 267.7522 361.8584 542.73093229 821.1595351 988.818290
#> Bent Cotyledon Mature Green
#> [1,] 2.128736 1.144999
#> [2,] 484.976400 12960.780277
#>
#> $Pentapetalae
#> Preglobular Globular Early Heart Late Heart Early Torpedo
#> [1,] 0.05261297 0.01197911 0.08091946 0.08694481 0.0982695
#> [2,] 635.42989937 495.34699334 417.37091062 317.80365833 272.6756148
#> Late Torpedo Bent Cotyledon Mature Green
#> [1,] 0.1884891 0.06334834 7.368801e-02
#> [2,] 209.1104428 87.99405005 2.482625e+03
#>
#> $Rosids
#> Preglobular Globular Early Heart Late Heart Early Torpedo Late Torpedo
#> [1,] 0.0000 0.0000 0.00000 0.00000 0.1432673 0.1435256
#> [2,] 642.4961 185.3317 91.70859 98.72456 147.6228087 103.7562025
#> Bent Cotyledon Mature Green
#> [1,] 2.773028 0.2618479
#> [2,] 41.354124 1199.1175298
#>
#> $Malvids
#> Preglobular Globular Early Heart Late Heart Early Torpedo Late Torpedo
#> [1,] 0.1975973 0.06982345 3.651396 13.90655 151.6683 115.2325
#> [2,] 0.1975973 0.06982345 3.651396 13.90655 151.6683 115.2325
#> Bent Cotyledon Mature Green
#> [1,] 273.8199 1376.466
#> [2,] 273.8199 1376.466
#>
#> $Brassicales
#> Preglobular Globular Early Heart Late Heart Early Torpedo Late Torpedo
#> [1,] 0.108494 0.01235082 0.4582448 2.966973 23.2142 44.6563
#> [2,] 1185.025172 632.57525785 475.6846959 524.167552 550.5373 878.1621
#> Bent Cotyledon Mature Green
#> [1,] 48.21886 9.177722
#> [2,] 1211.64171 13326.382738
#>
#> $Brassicaceae
#> Preglobular Globular Early Heart Late Heart Early Torpedo Late Torpedo
#> [1,] 2.576976e-02 0.00 0.000 9.689722e-03 1.217018e-02 7.805728e-02
#> [2,] 1.749544e+04 15175.64 7916.273 5.056297e+03 6.073790e+03 2.698556e+03
#> Bent Cotyledon Mature Green
#> [1,] 0.8951774 0.1766512
#> [2,] 1066.8117527 5174.1424821
#>
#> $Camelineae
#> Preglobular Globular Early Heart Late Heart Early Torpedo Late Torpedo
#> [1,] 103.8834 105.0861 74.49384 77.86892 123.7724 74.73676
#> [2,] 1322.0438 620.8688 797.86782 359.76975 932.8575 626.21049
#> Bent Cotyledon Mature Green
#> [1,] 28.42762 19.43867
#> [2,] 664.64225 1256.45665
#>
#> $Arabidopsis
#> Preglobular Globular Early Heart Late Heart Early Torpedo Late Torpedo
#> [1,] 0.06434192 0.0000 0.1530719 0.2052625 1.515649 5.95713
#> [2,] 841.28115092 414.7169 412.3216774 351.0940496 571.246363 445.54896
#> Bent Cotyledon Mature Green
#> [1,] 21.84301 30.71553
#> [2,] 455.03646 1117.21434
#>
#> $`Arabidopsis thaliana`
#> Preglobular Globular Early Heart Late Heart Early Torpedo Late Torpedo
#> [1,] 27.47878 24.27659 4.510751 5.873973 42.98079 37.08141
#> [2,] 118.24917 118.91433 97.911597 115.962891 127.05882 108.71476
#> Bent Cotyledon Mature Green
#> [1,] 22.26581 10.4845
#> [2,] 162.11333 398.9621
#>