computes the phylogenetically based transcriptome evolutionary index (TEI) shuffling the strata for permutation statistic

rcpp_boottei_parallel(expression, ps, permutations, ncores = 1L)

Arguments

expression

ExpressionSet as sparseMatrix

ps

named Phylostratum

permutations

number of permutations

ncores

number of cores

Value

sparseMatrix

Author

Kristian K Ullrich

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,] 3.564857 3.546878 3.537607 3.539186 3.485415 3.448678 3.494906
#>   [2,] 3.487805 3.521280 3.526633 3.528385 3.551820 3.535498 3.376304
#>   [3,] 3.518455 3.510498 3.560359 3.538537 3.549184 3.568732 3.595871
#>   [4,] 3.544712 3.543734 3.539996 3.546088 3.556953 3.591137 3.553157
#>   [5,] 3.555767 3.536314 3.582290 3.571278 3.555231 3.527897 3.587391
#>   [6,] 3.529871 3.555824 3.567427 3.554942 3.537854 3.519382 3.500499
#>   [7,] 3.548960 3.551891 3.555132 3.559540 3.556301 3.558915 3.457202
#>   [8,] 3.504526 3.518191 3.569446 3.538517 3.524009 3.517558 3.438521
#>   [9,] 3.538835 3.519371 3.540833 3.541580 3.540054 3.544102 3.499630
#>  [10,] 3.610834 3.591155 3.579011 3.589519 3.591724 3.585462 3.528572
#>  [11,] 3.512156 3.505304 3.533672 3.519147 3.508895 3.552554 3.594430
#>  [12,] 3.569689 3.544774 3.540196 3.549322 3.527876 3.527681 3.570266
#>  [13,] 3.521058 3.515946 3.543281 3.519187 3.543010 3.524855 3.450063
#>  [14,] 3.423963 3.415951 3.434335 3.433204 3.438623 3.450761 3.437898
#>  [15,] 3.477992 3.480891 3.458015 3.479906 3.468131 3.442521 3.496234
#>  [16,] 3.637902 3.638750 3.631563 3.621220 3.615538 3.611181 3.621064
#>  [17,] 3.484388 3.494179 3.520588 3.502073 3.514155 3.471817 3.476008
#>  [18,] 3.479200 3.464419 3.456521 3.454296 3.430403 3.441963 3.465384
#>  [19,] 3.506291 3.518907 3.506626 3.506491 3.503560 3.501926 3.517623
#>  [20,] 3.514125 3.504186 3.507593 3.519478 3.528205 3.509923 3.514987
#>  [21,] 3.433887 3.424459 3.431121 3.457017 3.475499 3.475879 3.487673
#>  [22,] 3.507037 3.523838 3.535264 3.542991 3.545170 3.563575 3.490683
#>  [23,] 3.496473 3.473303 3.508537 3.521334 3.502271 3.502986 3.532402
#>  [24,] 3.553285 3.569299 3.571706 3.592600 3.566000 3.568055 3.514652
#>  [25,] 3.440429 3.459694 3.464093 3.456347 3.468751 3.454976 3.404169
#>  [26,] 3.534868 3.516642 3.509329 3.494215 3.507794 3.519320 3.560544
#>  [27,] 3.436281 3.456443 3.470099 3.481503 3.492420 3.462937 3.442537
#>  [28,] 3.534061 3.553091 3.538558 3.539311 3.549339 3.523308 3.569895
#>  [29,] 3.490605 3.488311 3.507607 3.503777 3.501605 3.478606 3.492860
#>  [30,] 3.455304 3.465141 3.499801 3.503244 3.513699 3.563767 3.587987
#>  [31,] 3.519105 3.520089 3.523259 3.529454 3.562086 3.564197 3.555092
#>  [32,] 3.501081 3.492848 3.454427 3.468040 3.449816 3.451514 3.512670
#>  [33,] 3.465349 3.507456 3.535029 3.528958 3.544888 3.519611 3.528556
#>  [34,] 3.453393 3.453777 3.469306 3.474998 3.481338 3.473180 3.480104
#>  [35,] 3.543587 3.554303 3.545314 3.528677 3.539038 3.548451 3.621660
#>  [36,] 3.485089 3.503122 3.533548 3.523029 3.511133 3.530368 3.470067
#>  [37,] 3.447218 3.433500 3.433584 3.450701 3.446561 3.451302 3.529246
#>  [38,] 3.521971 3.505895 3.504710 3.491191 3.508982 3.501947 3.513565
#>  [39,] 3.580010 3.586123 3.593853 3.588472 3.577342 3.530508 3.519101
#>  [40,] 3.497515 3.501667 3.494773 3.485657 3.495254 3.485684 3.448149
#>  [41,] 3.579868 3.608473 3.597736 3.595242 3.609676 3.605934 3.547354
#>  [42,] 3.557344 3.552230 3.600598 3.604746 3.610638 3.589447 3.491396
#>  [43,] 3.438241 3.449442 3.453776 3.470590 3.461758 3.474828 3.485511
#>  [44,] 3.565224 3.572740 3.554598 3.550743 3.538126 3.527285 3.558003
#>  [45,] 3.470353 3.466090 3.496853 3.483403 3.495525 3.512020 3.491664
#>  [46,] 3.463626 3.494529 3.448753 3.439578 3.406020 3.381665 3.365055
#>  [47,] 3.509088 3.504344 3.466291 3.472652 3.470345 3.469572 3.463890
#>  [48,] 3.480162 3.491324 3.463888 3.480979 3.514214 3.487655 3.508733
#>  [49,] 3.519606 3.545516 3.586535 3.572383 3.554404 3.518705 3.514517
#>  [50,] 3.478928 3.492326 3.531085 3.525203 3.521316 3.502755 3.484907
#>  [51,] 3.522885 3.530210 3.545714 3.537466 3.521028 3.513107 3.509116
#>  [52,] 3.510506 3.506614 3.470443 3.471221 3.478710 3.450060 3.486659
#>  [53,] 3.597909 3.595303 3.634583 3.638482 3.623449 3.627894 3.614251
#>  [54,] 3.475896 3.455422 3.426618 3.430416 3.433126 3.438051 3.496178
#>  [55,] 3.541991 3.532741 3.505131 3.496995 3.473565 3.507143 3.464256
#>  [56,] 3.605078 3.580429 3.555573 3.537775 3.512733 3.493375 3.564237
#>  [57,] 3.480521 3.484995 3.499799 3.490383 3.457493 3.480869 3.476583
#>  [58,] 3.499185 3.512148 3.486278 3.493146 3.498918 3.533074 3.566297
#>  [59,] 3.524059 3.529228 3.518435 3.526531 3.541807 3.541599 3.485564
#>  [60,] 3.456356 3.466452 3.457408 3.428219 3.411452 3.406871 3.437986
#>  [61,] 3.510844 3.512818 3.525216 3.522339 3.517393 3.501450 3.548385
#>  [62,] 3.493781 3.513605 3.538352 3.534938 3.540455 3.529816 3.410968
#>  [63,] 3.446737 3.464834 3.478442 3.458268 3.471175 3.462530 3.400694
#>  [64,] 3.548914 3.569658 3.546747 3.562884 3.542888 3.521533 3.609666
#>  [65,] 3.507561 3.504247 3.498418 3.506433 3.512272 3.515184 3.564852
#>  [66,] 3.579046 3.587055 3.570543 3.592944 3.593627 3.590939 3.535563
#>  [67,] 3.438492 3.442398 3.422142 3.433553 3.439072 3.447034 3.435734
#>  [68,] 3.426428 3.435662 3.412906 3.431832 3.445870 3.430040 3.439134
#>  [69,] 3.543606 3.511521 3.441281 3.469579 3.446106 3.458361 3.518603
#>  [70,] 3.505515 3.500842 3.519855 3.519933 3.509782 3.496122 3.492556
#>  [71,] 3.533325 3.540524 3.522387 3.530371 3.551214 3.549546 3.523298
#>  [72,] 3.468503 3.472513 3.459832 3.474773 3.505181 3.547326 3.461297
#>  [73,] 3.586831 3.595617 3.582072 3.590050 3.601832 3.603889 3.565115
#>  [74,] 3.539700 3.540133 3.541079 3.519874 3.533518 3.521605 3.548748
#>  [75,] 3.537184 3.549946 3.542442 3.544951 3.523284 3.534818 3.477928
#>  [76,] 3.545979 3.534617 3.533452 3.553552 3.587663 3.561449 3.533211
#>  [77,] 3.552854 3.550811 3.530698 3.532745 3.548853 3.512535 3.494194
#>  [78,] 3.425080 3.426642 3.457077 3.458242 3.472050 3.499595 3.528484
#>  [79,] 3.467619 3.490611 3.511373 3.511624 3.501065 3.520745 3.566879
#>  [80,] 3.524901 3.534891 3.535314 3.534231 3.543330 3.526250 3.502701
#>  [81,] 3.564499 3.545249 3.502799 3.513186 3.485105 3.458969 3.524702
#>  [82,] 3.477192 3.493509 3.505979 3.509054 3.495323 3.447548 3.416452
#>  [83,] 3.491140 3.447743 3.417402 3.426169 3.446959 3.469218 3.512710
#>  [84,] 3.600856 3.640311 3.617556 3.595277 3.602943 3.600435 3.572013
#>  [85,] 3.498644 3.497811 3.475042 3.471090 3.463358 3.484960 3.552452
#>  [86,] 3.465871 3.474604 3.474425 3.485490 3.465310 3.441576 3.423083
#>  [87,] 3.467626 3.471980 3.506959 3.503053 3.493166 3.434489 3.426546
#>  [88,] 3.490995 3.480104 3.482968 3.490854 3.501702 3.526720 3.508184
#>  [89,] 3.492241 3.489019 3.489544 3.504110 3.504167 3.552802 3.585236
#>  [90,] 3.465619 3.467156 3.476465 3.485933 3.484512 3.478716 3.525312
#>  [91,] 3.476097 3.503502 3.504010 3.479512 3.477316 3.521556 3.407871
#>  [92,] 3.568063 3.559642 3.591898 3.583279 3.561938 3.538173 3.579768
#>  [93,] 3.503382 3.506616 3.561515 3.570330 3.573259 3.559919 3.597052
#>  [94,] 3.541182 3.532528 3.545915 3.566763 3.561681 3.553035 3.566538
#>  [95,] 3.533912 3.538940 3.535342 3.542470 3.576426 3.603088 3.557510
#>  [96,] 3.381266 3.399151 3.431256 3.441911 3.433889 3.427174 3.539137
#>  [97,] 3.506912 3.514171 3.539473 3.548437 3.563517 3.552916 3.486321
#>  [98,] 3.544970 3.551950 3.544126 3.513621 3.516165 3.545998 3.584266
#>  [99,] 3.524533 3.534032 3.584924 3.581543 3.525885 3.515222 3.592140
#> [100,] 3.593696 3.573896 3.565815 3.570087 3.537920 3.572316 3.585281