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,] 3.485065 3.500548 3.523695 3.513210 3.518488 3.536586 3.505940
#> [2,] 3.450433 3.456191 3.459595 3.454438 3.437657 3.480261 3.446454
#> [3,] 3.534142 3.534034 3.548797 3.550227 3.552603 3.554733 3.543461
#> [4,] 3.536101 3.533254 3.513446 3.524565 3.517994 3.557340 3.536497
#> [5,] 3.508651 3.518543 3.504199 3.540596 3.549397 3.552073 3.533044
#> [6,] 3.558369 3.546603 3.531305 3.539373 3.552368 3.537420 3.447822
#> [7,] 3.543463 3.539038 3.590499 3.559016 3.559545 3.572261 3.511127
#> [8,] 3.450836 3.446856 3.440262 3.426459 3.421018 3.428527 3.506781
#> [9,] 3.578727 3.576340 3.555575 3.558988 3.563689 3.556704 3.520515
#> [10,] 3.569295 3.550210 3.514895 3.517598 3.539634 3.556474 3.541706
#> [11,] 3.507978 3.525927 3.505090 3.510493 3.514511 3.457838 3.438887
#> [12,] 3.521401 3.520601 3.483204 3.490950 3.493933 3.505095 3.493845
#> [13,] 3.473782 3.475366 3.498906 3.519962 3.553547 3.536754 3.465897
#> [14,] 3.495975 3.494553 3.522059 3.510915 3.491990 3.486616 3.478194
#> [15,] 3.439812 3.418574 3.448768 3.460049 3.480807 3.480883 3.514986
#> [16,] 3.537144 3.511894 3.513971 3.531042 3.530224 3.571280 3.514913
#> [17,] 3.457717 3.446786 3.458322 3.483095 3.498497 3.517633 3.543894
#> [18,] 3.455554 3.447912 3.470496 3.462529 3.452899 3.494469 3.529821
#> [19,] 3.454914 3.469083 3.484552 3.491104 3.454225 3.452984 3.536013
#> [20,] 3.531732 3.547022 3.584379 3.581904 3.559391 3.546595 3.488368
#> [21,] 3.615637 3.569811 3.541041 3.537724 3.536676 3.523952 3.601040
#> [22,] 3.597227 3.607700 3.546949 3.550177 3.546260 3.548395 3.609069
#> [23,] 3.425372 3.423062 3.436914 3.427645 3.411498 3.442659 3.427586
#> [24,] 3.650197 3.627605 3.645724 3.651598 3.631273 3.660346 3.586527
#> [25,] 3.455602 3.472342 3.464089 3.464316 3.456929 3.437475 3.457195
#> [26,] 3.473583 3.495222 3.518632 3.498197 3.507131 3.513286 3.480314
#> [27,] 3.437233 3.422187 3.386025 3.382569 3.382434 3.352647 3.359759
#> [28,] 3.444755 3.449036 3.452384 3.452610 3.460757 3.540128 3.569811
#> [29,] 3.523749 3.533837 3.565080 3.535494 3.508461 3.494340 3.505571
#> [30,] 3.454379 3.436866 3.458962 3.470221 3.469511 3.493466 3.563412
#> [31,] 3.506344 3.548313 3.525084 3.498452 3.496660 3.475995 3.471965
#> [32,] 3.402017 3.382286 3.395447 3.411462 3.426799 3.440598 3.465712
#> [33,] 3.535107 3.495623 3.500223 3.503116 3.491167 3.515757 3.501457
#> [34,] 3.545782 3.527204 3.533275 3.541225 3.546722 3.557578 3.553596
#> [35,] 3.469558 3.466290 3.471240 3.470325 3.492974 3.496060 3.532502
#> [36,] 3.439787 3.463764 3.465573 3.465791 3.460079 3.451410 3.435245
#> [37,] 3.592363 3.609051 3.577068 3.579376 3.617450 3.614728 3.532373
#> [38,] 3.442015 3.444140 3.451190 3.463300 3.487857 3.502834 3.448861
#> [39,] 3.401813 3.404089 3.385019 3.384933 3.389660 3.382516 3.454582
#> [40,] 3.477130 3.477000 3.519266 3.505307 3.484813 3.491189 3.430860
#> [41,] 3.537599 3.509745 3.520441 3.525631 3.517660 3.519152 3.469915
#> [42,] 3.502789 3.519938 3.540519 3.533407 3.516727 3.519334 3.549323
#> [43,] 3.522362 3.512204 3.508342 3.514974 3.505605 3.498172 3.548005
#> [44,] 3.419094 3.449131 3.452715 3.461094 3.435231 3.447928 3.450133
#> [45,] 3.452982 3.447575 3.461756 3.476219 3.465800 3.461766 3.529605
#> [46,] 3.530784 3.535163 3.539798 3.526743 3.563731 3.574288 3.470460
#> [47,] 3.546035 3.549349 3.571674 3.580288 3.578451 3.585698 3.485385
#> [48,] 3.443652 3.436089 3.509961 3.489863 3.488037 3.495170 3.615633
#> [49,] 3.513142 3.508967 3.479432 3.494024 3.516489 3.536835 3.516466
#> [50,] 3.460031 3.452279 3.485304 3.500410 3.497081 3.499209 3.520941
#> [51,] 3.563983 3.536105 3.554214 3.568197 3.566877 3.592618 3.496183
#> [52,] 3.513813 3.507023 3.525951 3.522930 3.510582 3.493686 3.520616
#> [53,] 3.503404 3.499828 3.519098 3.508959 3.513663 3.538344 3.502143
#> [54,] 3.487687 3.477153 3.448287 3.456206 3.447132 3.423523 3.506686
#> [55,] 3.483835 3.472546 3.479919 3.502852 3.507656 3.497641 3.493258
#> [56,] 3.544301 3.551873 3.548581 3.549295 3.528093 3.508926 3.607338
#> [57,] 3.466352 3.488251 3.500020 3.497063 3.491411 3.472133 3.467444
#> [58,] 3.437950 3.467349 3.476617 3.462564 3.470358 3.439007 3.440881
#> [59,] 3.513794 3.513371 3.544162 3.563606 3.584393 3.616472 3.538583
#> [60,] 3.395633 3.407416 3.447300 3.448800 3.473976 3.456841 3.413727
#> [61,] 3.521370 3.527778 3.510665 3.516791 3.533563 3.530460 3.590304
#> [62,] 3.435900 3.439003 3.462339 3.469575 3.476532 3.446932 3.489802
#> [63,] 3.460701 3.478696 3.503909 3.497206 3.481968 3.477703 3.434062
#> [64,] 3.564472 3.552119 3.529966 3.540339 3.570445 3.574167 3.557788
#> [65,] 3.665218 3.641421 3.645443 3.643485 3.614275 3.566026 3.482296
#> [66,] 3.549158 3.545901 3.551212 3.539276 3.535103 3.511192 3.516926
#> [67,] 3.517841 3.520738 3.498495 3.488284 3.496990 3.462758 3.521473
#> [68,] 3.498910 3.525966 3.510460 3.525591 3.540729 3.531492 3.526949
#> [69,] 3.491820 3.502947 3.475760 3.492799 3.488865 3.470330 3.469068
#> [70,] 3.509015 3.516993 3.534962 3.522264 3.537645 3.544526 3.505181
#> [71,] 3.554149 3.534371 3.569309 3.579121 3.565091 3.533619 3.607779
#> [72,] 3.513397 3.515119 3.497527 3.500893 3.509220 3.500741 3.483599
#> [73,] 3.492957 3.487800 3.515289 3.500386 3.487112 3.542580 3.513061
#> [74,] 3.535984 3.531182 3.543331 3.561751 3.556978 3.577525 3.533953
#> [75,] 3.499591 3.488090 3.483900 3.493926 3.500501 3.531731 3.499708
#> [76,] 3.396401 3.375157 3.406631 3.402845 3.432941 3.487822 3.540748
#> [77,] 3.600023 3.620185 3.581089 3.578346 3.568079 3.571804 3.594126
#> [78,] 3.551101 3.541187 3.542033 3.552960 3.553655 3.534751 3.534068
#> [79,] 3.546061 3.538312 3.539328 3.518645 3.492269 3.497597 3.471863
#> [80,] 3.531713 3.527833 3.513508 3.517726 3.513249 3.563071 3.475138
#> [81,] 3.531367 3.530205 3.542648 3.525238 3.495363 3.525207 3.517780
#> [82,] 3.474114 3.503793 3.512647 3.493299 3.485726 3.477402 3.437767
#> [83,] 3.385961 3.407081 3.454082 3.452492 3.447172 3.448199 3.397078
#> [84,] 3.486110 3.508970 3.548654 3.524254 3.521531 3.543952 3.545779
#> [85,] 3.411092 3.428893 3.454040 3.465658 3.459026 3.466486 3.456636
#> [86,] 3.604336 3.577133 3.557696 3.542845 3.538461 3.568805 3.632620
#> [87,] 3.531275 3.516473 3.529812 3.506306 3.501487 3.521841 3.518759
#> [88,] 3.513079 3.499215 3.551186 3.546389 3.545731 3.561184 3.566536
#> [89,] 3.538608 3.544846 3.564917 3.525106 3.532875 3.558406 3.547311
#> [90,] 3.599651 3.616330 3.558358 3.568562 3.552894 3.532971 3.514893
#> [91,] 3.470882 3.482628 3.508899 3.520075 3.526829 3.571617 3.521389
#> [92,] 3.545927 3.548086 3.535224 3.559724 3.580593 3.612495 3.586157
#> [93,] 3.452810 3.452795 3.445646 3.451387 3.453661 3.475940 3.499907
#> [94,] 3.425632 3.417743 3.455482 3.465863 3.461739 3.451724 3.546973
#> [95,] 3.463940 3.484618 3.490187 3.484471 3.486134 3.513660 3.480674
#> [96,] 3.469190 3.474024 3.526860 3.511217 3.509974 3.468255 3.456542
#> [97,] 3.463207 3.465013 3.520461 3.526601 3.555582 3.562655 3.526191
#> [98,] 3.500710 3.500088 3.473551 3.478605 3.479792 3.494792 3.528789
#> [99,] 3.421468 3.421371 3.434253 3.445164 3.439634 3.424682 3.453375
#> [100,] 3.462148 3.449993 3.431413 3.435270 3.443673 3.455121 3.479393