computes the phylogenetically based transcriptome evolutionary index (TEI) shuffling the strata for permutation statistic
Examples
## 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,] 3.529637 3.543665 3.561488 3.534913 3.522338 3.553774 3.576086
#> [2,] 3.598492 3.610238 3.593814 3.599822 3.586416 3.591563 3.556110
#> [3,] 3.469476 3.481390 3.412909 3.422836 3.448166 3.451186 3.445650
#> [4,] 3.589494 3.560525 3.567055 3.570309 3.571313 3.561713 3.462836
#> [5,] 3.489302 3.480248 3.480732 3.484873 3.480947 3.452801 3.433960
#> [6,] 3.564855 3.569396 3.556580 3.554873 3.560536 3.566778 3.494452
#> [7,] 3.565866 3.554988 3.525023 3.534148 3.526615 3.538664 3.558267
#> [8,] 3.556153 3.545221 3.520126 3.538724 3.559238 3.569040 3.568834
#> [9,] 3.571453 3.571678 3.554703 3.561015 3.585528 3.611571 3.641196
#> [10,] 3.502619 3.475611 3.449604 3.455280 3.454411 3.468458 3.514334
#> [11,] 3.524752 3.515412 3.487802 3.499371 3.497843 3.508858 3.517038
#> [12,] 3.385475 3.389575 3.419393 3.411070 3.401314 3.395672 3.422704
#> [13,] 3.481269 3.472525 3.474655 3.482179 3.481566 3.494566 3.616880
#> [14,] 3.526381 3.501413 3.519743 3.525546 3.533915 3.549754 3.563901
#> [15,] 3.560876 3.552870 3.545861 3.528217 3.534874 3.530958 3.512062
#> [16,] 3.566046 3.570620 3.568354 3.569348 3.558810 3.553935 3.580916
#> [17,] 3.596811 3.594284 3.574915 3.593985 3.617756 3.568816 3.480330
#> [18,] 3.500121 3.528065 3.507163 3.496477 3.503878 3.541527 3.459056
#> [19,] 3.611126 3.620425 3.597928 3.607611 3.578518 3.530719 3.616022
#> [20,] 3.475816 3.513152 3.533741 3.513324 3.504373 3.491539 3.364441
#> [21,] 3.523369 3.493395 3.509687 3.508239 3.517911 3.503556 3.521473
#> [22,] 3.398154 3.415312 3.459079 3.464700 3.496530 3.490219 3.475619
#> [23,] 3.567315 3.584816 3.583347 3.568440 3.556064 3.545710 3.567624
#> [24,] 3.495331 3.508147 3.518300 3.528141 3.529339 3.525139 3.487775
#> [25,] 3.575392 3.575685 3.583623 3.593355 3.622394 3.625690 3.536319
#> [26,] 3.467121 3.493086 3.498849 3.485393 3.481271 3.445919 3.543956
#> [27,] 3.540871 3.525494 3.496533 3.516278 3.505367 3.488084 3.501820
#> [28,] 3.563703 3.543798 3.550075 3.579181 3.570081 3.631393 3.664289
#> [29,] 3.575127 3.590265 3.616038 3.590471 3.587732 3.528740 3.545334
#> [30,] 3.533445 3.532242 3.536852 3.551705 3.531397 3.517448 3.612483
#> [31,] 3.507747 3.494562 3.505291 3.507544 3.496963 3.480126 3.569062
#> [32,] 3.495905 3.511389 3.508936 3.520761 3.535780 3.528939 3.487192
#> [33,] 3.487868 3.489066 3.537125 3.531472 3.503684 3.527261 3.529977
#> [34,] 3.525052 3.489881 3.474748 3.482030 3.496279 3.510789 3.547183
#> [35,] 3.529114 3.507521 3.471859 3.470324 3.476561 3.462387 3.573692
#> [36,] 3.478000 3.486599 3.495004 3.492946 3.498465 3.497268 3.484198
#> [37,] 3.565900 3.530726 3.514657 3.526292 3.527154 3.484632 3.486690
#> [38,] 3.425283 3.444069 3.427559 3.436271 3.438466 3.486840 3.463642
#> [39,] 3.489425 3.511038 3.523039 3.513338 3.495303 3.507013 3.527133
#> [40,] 3.570136 3.583468 3.594685 3.587916 3.558065 3.527709 3.494532
#> [41,] 3.477544 3.489007 3.524433 3.517616 3.501072 3.474706 3.447690
#> [42,] 3.559078 3.539042 3.536971 3.521318 3.496056 3.471866 3.423912
#> [43,] 3.452184 3.447558 3.452325 3.465353 3.477599 3.506349 3.515703
#> [44,] 3.596064 3.586892 3.560422 3.554600 3.571377 3.571468 3.631984
#> [45,] 3.540613 3.531618 3.530182 3.544689 3.569044 3.582675 3.613797
#> [46,] 3.397352 3.420822 3.452160 3.463692 3.457666 3.428891 3.397931
#> [47,] 3.377340 3.402608 3.402559 3.380984 3.382453 3.425066 3.384040
#> [48,] 3.489349 3.478134 3.481873 3.485382 3.479949 3.476975 3.498736
#> [49,] 3.455268 3.449261 3.451845 3.433137 3.448098 3.465907 3.486934
#> [50,] 3.557914 3.526096 3.501492 3.502784 3.513269 3.514570 3.569819
#> [51,] 3.535869 3.517194 3.517952 3.514285 3.529466 3.519479 3.462140
#> [52,] 3.439138 3.426112 3.462366 3.453630 3.470264 3.475698 3.552712
#> [53,] 3.486587 3.512747 3.508200 3.504546 3.542109 3.517135 3.473381
#> [54,] 3.465074 3.439019 3.475122 3.485781 3.467558 3.439619 3.410395
#> [55,] 3.471893 3.479427 3.486317 3.486074 3.456751 3.465674 3.462534
#> [56,] 3.585226 3.555278 3.536224 3.558330 3.570254 3.623955 3.580354
#> [57,] 3.603669 3.598603 3.548510 3.536458 3.506575 3.502893 3.517387
#> [58,] 3.472374 3.476019 3.467644 3.448289 3.432634 3.466822 3.460099
#> [59,] 3.477599 3.459364 3.470410 3.452052 3.444157 3.444674 3.498882
#> [60,] 3.529399 3.506688 3.503887 3.504808 3.489063 3.485537 3.534155
#> [61,] 3.554485 3.537360 3.502376 3.501790 3.495085 3.491549 3.482117
#> [62,] 3.472904 3.470934 3.486492 3.493772 3.494295 3.486886 3.457115
#> [63,] 3.549780 3.554742 3.515971 3.511072 3.522473 3.506866 3.473658
#> [64,] 3.429894 3.414975 3.436516 3.440741 3.428362 3.445714 3.479321
#> [65,] 3.614564 3.604378 3.606096 3.617367 3.598930 3.584802 3.512540
#> [66,] 3.554701 3.580263 3.597792 3.562749 3.573932 3.577384 3.573432
#> [67,] 3.549213 3.528722 3.519965 3.551919 3.558248 3.595287 3.530565
#> [68,] 3.491638 3.467271 3.462208 3.465486 3.484012 3.563883 3.632719
#> [69,] 3.558385 3.585313 3.603388 3.578914 3.574177 3.540735 3.580819
#> [70,] 3.512625 3.514842 3.538854 3.519829 3.501359 3.469934 3.560838
#> [71,] 3.526533 3.534181 3.529271 3.515078 3.496311 3.517238 3.530615
#> [72,] 3.598541 3.582771 3.573233 3.543785 3.559681 3.567651 3.480074
#> [73,] 3.452050 3.457902 3.451257 3.461642 3.476809 3.471083 3.382474
#> [74,] 3.554019 3.553600 3.501602 3.505576 3.490093 3.477475 3.526113
#> [75,] 3.506754 3.516188 3.529717 3.528195 3.557641 3.584173 3.531771
#> [76,] 3.627820 3.618010 3.518882 3.518608 3.536243 3.543571 3.517118
#> [77,] 3.609720 3.594420 3.567382 3.573599 3.591641 3.588550 3.548869
#> [78,] 3.464149 3.476222 3.502396 3.494963 3.497939 3.487674 3.442769
#> [79,] 3.513510 3.502181 3.539516 3.535466 3.535528 3.567471 3.642517
#> [80,] 3.506983 3.491729 3.515344 3.535606 3.517234 3.498794 3.534841
#> [81,] 3.473652 3.461513 3.458530 3.465295 3.460796 3.445996 3.524260
#> [82,] 3.724204 3.729790 3.654938 3.640534 3.608803 3.612377 3.576418
#> [83,] 3.518164 3.525081 3.509478 3.514791 3.506614 3.499583 3.561611
#> [84,] 3.594728 3.607641 3.596039 3.581419 3.543593 3.541691 3.516445
#> [85,] 3.581114 3.591390 3.596872 3.580669 3.564697 3.570152 3.617684
#> [86,] 3.502373 3.528324 3.523527 3.495243 3.485147 3.470434 3.431557
#> [87,] 3.530922 3.525984 3.548417 3.564090 3.535318 3.518476 3.620604
#> [88,] 3.455342 3.437263 3.436769 3.438135 3.436058 3.456654 3.532155
#> [89,] 3.550872 3.536093 3.532643 3.542573 3.531872 3.546281 3.490834
#> [90,] 3.536925 3.554549 3.562145 3.549896 3.546865 3.534202 3.555221
#> [91,] 3.571383 3.548751 3.540661 3.557277 3.577023 3.579147 3.567687
#> [92,] 3.555729 3.572121 3.575588 3.564472 3.552864 3.523677 3.562440
#> [93,] 3.431691 3.457664 3.452842 3.439575 3.478553 3.462568 3.420578
#> [94,] 3.527449 3.533818 3.537857 3.520803 3.500547 3.507985 3.487098
#> [95,] 3.507445 3.514061 3.457632 3.460020 3.466017 3.461206 3.477151
#> [96,] 3.559770 3.553942 3.527359 3.522173 3.499022 3.512943 3.531690
#> [97,] 3.627922 3.596899 3.565827 3.565664 3.553277 3.569622 3.628509
#> [98,] 3.604967 3.611488 3.612766 3.628321 3.605392 3.620492 3.533323
#> [99,] 3.499076 3.508707 3.501564 3.495618 3.495362 3.546186 3.560589
#> [100,] 3.535311 3.563347 3.547359 3.553121 3.552502 3.551116 3.550360