computes the phylogenetically based transcriptome evolutionary index (TEI) shuffling the strata for permutation statistic
sparseMatrix
## load example PhyloExpressionSetExample
data("PhyloExpressionSetExample", package="myTAI")
## convert into sparseMatrix - rownames GeneID
spmat <- as(data.matrix(PhyloExpressionSetExample[,-c(1,2)]),
"sparseMatrix")
rownames(spmat) <- PhyloExpressionSetExample$GeneID
## create named Phylostratum vector
ps <- setNames(PhyloExpressionSetExample$Phylostratum,
PhyloExpressionSetExample$GeneID)
## get permutations
rcpp_boottei_parallel(spmat, ps, 100, 1)
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7]
#> [1,] 3.503089 3.506386 3.517082 3.506751 3.484894 3.495537 3.474207
#> [2,] 3.558718 3.586313 3.593821 3.593750 3.559076 3.554581 3.594720
#> [3,] 3.519737 3.513532 3.527028 3.538994 3.519226 3.548369 3.583673
#> [4,] 3.423165 3.427345 3.472623 3.468861 3.475284 3.466999 3.532411
#> [5,] 3.426491 3.441553 3.489327 3.478577 3.484201 3.442908 3.365268
#> [6,] 3.526736 3.537811 3.529298 3.530376 3.524876 3.533320 3.521789
#> [7,] 3.513950 3.514791 3.537845 3.515262 3.509976 3.533498 3.487408
#> [8,] 3.522056 3.499495 3.507699 3.519619 3.509914 3.507081 3.544538
#> [9,] 3.590315 3.562384 3.565646 3.566051 3.565853 3.573916 3.525156
#> [10,] 3.591417 3.567222 3.561729 3.553062 3.533891 3.544842 3.506917
#> [11,] 3.483025 3.481814 3.491260 3.483696 3.487496 3.482166 3.447072
#> [12,] 3.454349 3.421815 3.454578 3.453695 3.453106 3.498706 3.503429
#> [13,] 3.482028 3.465463 3.480887 3.485731 3.489307 3.494227 3.476940
#> [14,] 3.481448 3.500083 3.527176 3.539922 3.543124 3.502366 3.439895
#> [15,] 3.539864 3.557612 3.579742 3.589369 3.590361 3.551615 3.496322
#> [16,] 3.439322 3.452391 3.442022 3.454159 3.446171 3.447975 3.424542
#> [17,] 3.529392 3.572510 3.574100 3.540456 3.540005 3.496655 3.509575
#> [18,] 3.507186 3.512182 3.532505 3.549513 3.568154 3.600851 3.545704
#> [19,] 3.532462 3.529392 3.534951 3.546711 3.558664 3.562320 3.547502
#> [20,] 3.447386 3.477233 3.506977 3.494341 3.448348 3.447244 3.482986
#> [21,] 3.541309 3.558058 3.573554 3.544057 3.536774 3.568525 3.584717
#> [22,] 3.502381 3.503825 3.515470 3.516246 3.538476 3.545867 3.482529
#> [23,] 3.456761 3.472470 3.478824 3.481532 3.471601 3.455889 3.526871
#> [24,] 3.483765 3.482546 3.471043 3.479272 3.459137 3.457701 3.502754
#> [25,] 3.665778 3.651686 3.635182 3.634132 3.624238 3.633620 3.549160
#> [26,] 3.511734 3.489603 3.462436 3.467681 3.454076 3.425306 3.517267
#> [27,] 3.573594 3.551755 3.552762 3.572658 3.564377 3.527066 3.479172
#> [28,] 3.409819 3.403712 3.424073 3.443631 3.460282 3.460706 3.438310
#> [29,] 3.453439 3.413565 3.429571 3.449701 3.437678 3.470430 3.511186
#> [30,] 3.474017 3.481388 3.486463 3.488657 3.497855 3.502675 3.472998
#> [31,] 3.571926 3.585062 3.598471 3.561353 3.555769 3.547665 3.502352
#> [32,] 3.395841 3.394885 3.445090 3.447186 3.457041 3.445263 3.444048
#> [33,] 3.603830 3.611441 3.644529 3.639140 3.638343 3.617019 3.530743
#> [34,] 3.516354 3.504342 3.524664 3.543947 3.544708 3.515927 3.500000
#> [35,] 3.494675 3.475956 3.497582 3.521256 3.536336 3.551811 3.551395
#> [36,] 3.533783 3.528743 3.488667 3.481005 3.484910 3.523587 3.576452
#> [37,] 3.437120 3.445267 3.454987 3.459574 3.436736 3.411143 3.325307
#> [38,] 3.410513 3.444576 3.438551 3.420929 3.438741 3.456690 3.420352
#> [39,] 3.549879 3.536280 3.535134 3.533012 3.506721 3.506370 3.489827
#> [40,] 3.568782 3.571454 3.563000 3.562651 3.534895 3.532635 3.525590
#> [41,] 3.578458 3.569323 3.517951 3.508079 3.519831 3.470734 3.473841
#> [42,] 3.510442 3.502884 3.504909 3.487498 3.464995 3.456450 3.411218
#> [43,] 3.472197 3.460373 3.457806 3.462564 3.447611 3.461881 3.495429
#> [44,] 3.583693 3.604127 3.610088 3.593087 3.600404 3.575173 3.531962
#> [45,] 3.503698 3.490997 3.500452 3.504047 3.523847 3.514048 3.439425
#> [46,] 3.471260 3.461740 3.458068 3.439488 3.421917 3.399938 3.454455
#> [47,] 3.504725 3.509571 3.464217 3.476265 3.494067 3.520664 3.617601
#> [48,] 3.533426 3.525411 3.542982 3.547978 3.515033 3.461817 3.507687
#> [49,] 3.478731 3.463997 3.476646 3.473142 3.467581 3.477320 3.426602
#> [50,] 3.450415 3.485463 3.496244 3.473821 3.479445 3.509808 3.509548
#> [51,] 3.552252 3.541668 3.521645 3.534334 3.529753 3.532820 3.561494
#> [52,] 3.473052 3.483278 3.502108 3.492757 3.491002 3.499429 3.436094
#> [53,] 3.579535 3.574519 3.591154 3.583743 3.585089 3.593525 3.573667
#> [54,] 3.515684 3.512741 3.504664 3.493864 3.474001 3.504951 3.577404
#> [55,] 3.507558 3.511395 3.527882 3.524225 3.511194 3.514396 3.489733
#> [56,] 3.494053 3.514475 3.508938 3.494909 3.504027 3.518307 3.497414
#> [57,] 3.516481 3.492083 3.586445 3.569125 3.550765 3.546990 3.582254
#> [58,] 3.624835 3.609254 3.620168 3.624113 3.633196 3.653314 3.564626
#> [59,] 3.409662 3.409362 3.412023 3.422434 3.424108 3.423280 3.443547
#> [60,] 3.454231 3.455066 3.469616 3.481938 3.493387 3.494004 3.468418
#> [61,] 3.536431 3.580142 3.578352 3.568305 3.538807 3.521931 3.503674
#> [62,] 3.527575 3.533310 3.525931 3.526127 3.533262 3.520551 3.476473
#> [63,] 3.449066 3.460940 3.507531 3.503203 3.494344 3.538224 3.557132
#> [64,] 3.504472 3.478505 3.505094 3.523514 3.552586 3.574856 3.573713
#> [65,] 3.666629 3.657965 3.710347 3.725850 3.707877 3.691316 3.617200
#> [66,] 3.475454 3.472410 3.502564 3.499041 3.494817 3.462919 3.524631
#> [67,] 3.539784 3.509249 3.557217 3.550342 3.550501 3.553612 3.538478
#> [68,] 3.527953 3.532181 3.503217 3.509741 3.520289 3.508203 3.475679
#> [69,] 3.553945 3.528471 3.554441 3.545325 3.515503 3.523796 3.572552
#> [70,] 3.452354 3.442132 3.449131 3.451320 3.446831 3.410632 3.456422
#> [71,] 3.569690 3.571566 3.587564 3.573689 3.562377 3.562119 3.603515
#> [72,] 3.441872 3.436570 3.432100 3.439857 3.456018 3.474272 3.464395
#> [73,] 3.516298 3.518101 3.531206 3.535488 3.530376 3.549901 3.578273
#> [74,] 3.576156 3.585322 3.582830 3.570528 3.569078 3.546528 3.531019
#> [75,] 3.518908 3.518174 3.547900 3.533456 3.541592 3.523344 3.466030
#> [76,] 3.536198 3.526903 3.566746 3.563345 3.566843 3.554232 3.561795
#> [77,] 3.489121 3.495301 3.470676 3.461995 3.461616 3.475031 3.571446
#> [78,] 3.482182 3.478440 3.480132 3.478889 3.487499 3.503001 3.496735
#> [79,] 3.618774 3.593987 3.599722 3.617649 3.635575 3.636303 3.610570
#> [80,] 3.527213 3.512056 3.504497 3.499223 3.509588 3.532204 3.518668
#> [81,] 3.493334 3.522964 3.480338 3.466777 3.455369 3.426874 3.388173
#> [82,] 3.508352 3.509922 3.437525 3.422804 3.423454 3.393632 3.482232
#> [83,] 3.543195 3.547814 3.540793 3.536459 3.549477 3.495272 3.475360
#> [84,] 3.403603 3.425822 3.417892 3.402901 3.419346 3.453193 3.364072
#> [85,] 3.523648 3.525879 3.517828 3.523133 3.535175 3.507600 3.410814
#> [86,] 3.476091 3.499286 3.476675 3.490094 3.515583 3.527244 3.511479
#> [87,] 3.489305 3.496051 3.485231 3.480378 3.497341 3.501714 3.515912
#> [88,] 3.540592 3.520083 3.536515 3.541391 3.575998 3.577567 3.562177
#> [89,] 3.463231 3.431871 3.415326 3.410048 3.407692 3.412750 3.458426
#> [90,] 3.564396 3.563779 3.527962 3.543443 3.530881 3.558172 3.617586
#> [91,] 3.561324 3.544255 3.554565 3.562760 3.545267 3.541571 3.515951
#> [92,] 3.577890 3.572002 3.614714 3.609894 3.598746 3.542397 3.526628
#> [93,] 3.537603 3.545941 3.538086 3.535941 3.556440 3.541692 3.503917
#> [94,] 3.468388 3.483191 3.502992 3.479933 3.477985 3.507960 3.599315
#> [95,] 3.402960 3.397191 3.425010 3.454697 3.463102 3.459901 3.460532
#> [96,] 3.582775 3.577832 3.559759 3.564060 3.553543 3.568022 3.595349
#> [97,] 3.621971 3.618609 3.575952 3.560495 3.559141 3.554093 3.505567
#> [98,] 3.503193 3.519862 3.480600 3.474358 3.484990 3.482844 3.409413
#> [99,] 3.444200 3.410250 3.400497 3.399467 3.404382 3.430123 3.468812
#> [100,] 3.531959 3.551251 3.549049 3.556393 3.535320 3.522240 3.534514