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,] 3.596030 3.599771 3.573075 3.555660 3.550978 3.541404 3.521604
#> [2,] 3.454304 3.477112 3.487254 3.487302 3.486822 3.463355 3.412541
#> [3,] 3.564814 3.550827 3.546132 3.551443 3.540314 3.507319 3.458141
#> [4,] 3.541647 3.524685 3.484168 3.496832 3.500821 3.537779 3.546029
#> [5,] 3.458286 3.455264 3.442472 3.448345 3.471962 3.445897 3.436929
#> [6,] 3.471238 3.445382 3.413288 3.418597 3.401160 3.405282 3.412054
#> [7,] 3.455521 3.446359 3.452927 3.448011 3.452938 3.469781 3.484841
#> [8,] 3.593911 3.613305 3.605454 3.629661 3.659906 3.675033 3.640471
#> [9,] 3.605469 3.611832 3.610676 3.614048 3.582676 3.583086 3.544488
#> [10,] 3.480722 3.471757 3.496574 3.492027 3.492693 3.513474 3.529391
#> [11,] 3.480082 3.518840 3.536260 3.539505 3.528685 3.549941 3.475960
#> [12,] 3.597266 3.607340 3.593628 3.570417 3.557507 3.535554 3.543235
#> [13,] 3.502438 3.480943 3.492797 3.503237 3.501605 3.504854 3.580714
#> [14,] 3.443934 3.448006 3.449135 3.437415 3.475097 3.494301 3.473749
#> [15,] 3.555568 3.535214 3.515855 3.519235 3.498130 3.513146 3.551252
#> [16,] 3.588309 3.598516 3.612394 3.592093 3.591033 3.615155 3.639692
#> [17,] 3.552934 3.528068 3.505657 3.499610 3.501400 3.543986 3.502912
#> [18,] 3.500893 3.530619 3.548551 3.539213 3.540415 3.544573 3.469080
#> [19,] 3.558910 3.560030 3.557913 3.537124 3.534886 3.539403 3.525891
#> [20,] 3.486720 3.504031 3.516955 3.507443 3.529115 3.502385 3.477258
#> [21,] 3.495756 3.499648 3.486198 3.469986 3.485882 3.546484 3.552649
#> [22,] 3.533537 3.497430 3.470141 3.481756 3.471996 3.516124 3.570606
#> [23,] 3.463184 3.464850 3.474864 3.463633 3.433107 3.443712 3.427959
#> [24,] 3.495680 3.518788 3.515610 3.509988 3.523998 3.574634 3.547637
#> [25,] 3.530720 3.518098 3.490709 3.516017 3.520600 3.588104 3.614589
#> [26,] 3.489871 3.495469 3.504806 3.499803 3.496194 3.477438 3.549763
#> [27,] 3.475631 3.463937 3.474011 3.444475 3.412960 3.420014 3.475061
#> [28,] 3.491257 3.492913 3.501091 3.500752 3.507967 3.493458 3.554800
#> [29,] 3.559039 3.536425 3.504274 3.508992 3.519145 3.501554 3.560050
#> [30,] 3.438524 3.450479 3.439990 3.428833 3.414812 3.437339 3.484989
#> [31,] 3.468428 3.476526 3.509817 3.533113 3.542874 3.522480 3.488622
#> [32,] 3.512016 3.528824 3.558062 3.540877 3.525507 3.483533 3.454497
#> [33,] 3.402906 3.403606 3.400978 3.424600 3.437897 3.440197 3.436487
#> [34,] 3.483939 3.480719 3.503411 3.517369 3.518775 3.516776 3.505605
#> [35,] 3.506523 3.508315 3.520713 3.516591 3.501174 3.504421 3.474627
#> [36,] 3.486522 3.475607 3.472748 3.458358 3.445869 3.472282 3.465794
#> [37,] 3.538076 3.535935 3.481675 3.492377 3.485125 3.499595 3.618797
#> [38,] 3.527561 3.547162 3.524593 3.503842 3.533709 3.506852 3.435001
#> [39,] 3.553567 3.529370 3.545298 3.552499 3.535211 3.532886 3.527848
#> [40,] 3.542256 3.565039 3.577228 3.585827 3.578683 3.575054 3.604722
#> [41,] 3.537926 3.539153 3.510979 3.524283 3.539450 3.493279 3.528770
#> [42,] 3.505068 3.503950 3.494272 3.493935 3.493476 3.504050 3.525494
#> [43,] 3.543672 3.547707 3.537210 3.517511 3.508834 3.523775 3.497568
#> [44,] 3.483025 3.464583 3.461080 3.477123 3.485223 3.462205 3.479391
#> [45,] 3.561231 3.552109 3.529156 3.539318 3.519588 3.533001 3.544838
#> [46,] 3.418936 3.427409 3.450865 3.460211 3.468617 3.464976 3.514299
#> [47,] 3.399535 3.429800 3.455460 3.444448 3.451693 3.454421 3.469928
#> [48,] 3.523577 3.509322 3.526275 3.516985 3.513352 3.539398 3.528435
#> [49,] 3.544693 3.544603 3.531760 3.536899 3.522398 3.520074 3.506346
#> [50,] 3.566292 3.564723 3.548462 3.567942 3.568322 3.537009 3.454590
#> [51,] 3.545837 3.539133 3.513916 3.510802 3.489468 3.519495 3.528267
#> [52,] 3.567878 3.572067 3.598746 3.579789 3.594126 3.585787 3.589477
#> [53,] 3.496850 3.477697 3.449823 3.453090 3.422652 3.401777 3.480673
#> [54,] 3.509565 3.484732 3.512063 3.522248 3.501402 3.534270 3.564162
#> [55,] 3.480350 3.500674 3.525408 3.510190 3.511106 3.516958 3.459290
#> [56,] 3.502845 3.486215 3.482729 3.502368 3.516369 3.492276 3.485211
#> [57,] 3.419851 3.435723 3.474836 3.475058 3.481275 3.524877 3.478445
#> [58,] 3.466333 3.466165 3.498792 3.475328 3.457886 3.462732 3.470097
#> [59,] 3.517877 3.536367 3.532041 3.555087 3.555589 3.555392 3.465083
#> [60,] 3.493958 3.474788 3.443321 3.448658 3.475156 3.484632 3.483299
#> [61,] 3.461118 3.455763 3.462790 3.466192 3.454698 3.460468 3.526246
#> [62,] 3.439188 3.418866 3.384931 3.395624 3.425189 3.490113 3.505074
#> [63,] 3.547335 3.555002 3.554951 3.547787 3.576938 3.581845 3.663258
#> [64,] 3.544368 3.547203 3.521450 3.506365 3.496367 3.509636 3.528597
#> [65,] 3.486153 3.496600 3.487772 3.466243 3.450155 3.449465 3.544152
#> [66,] 3.599618 3.600406 3.567476 3.574740 3.567237 3.553822 3.570929
#> [67,] 3.546991 3.532807 3.554998 3.553544 3.550061 3.572126 3.558513
#> [68,] 3.537954 3.540740 3.526334 3.534225 3.540603 3.515143 3.541243
#> [69,] 3.515554 3.532968 3.505715 3.504245 3.503528 3.508889 3.473687
#> [70,] 3.470344 3.485038 3.475754 3.474949 3.483934 3.498412 3.545996
#> [71,] 3.488348 3.509765 3.512935 3.505798 3.533777 3.504190 3.529255
#> [72,] 3.482375 3.494058 3.562122 3.558679 3.576951 3.607772 3.555395
#> [73,] 3.599814 3.621091 3.620932 3.598459 3.584691 3.569356 3.551996
#> [74,] 3.552090 3.546378 3.521278 3.518566 3.558347 3.535912 3.484808
#> [75,] 3.417669 3.420368 3.418628 3.418878 3.413265 3.413396 3.495657
#> [76,] 3.446329 3.442421 3.411687 3.426770 3.445860 3.437002 3.430960
#> [77,] 3.523063 3.505866 3.490467 3.500839 3.482179 3.453030 3.483078
#> [78,] 3.498345 3.472432 3.489998 3.483729 3.468112 3.463272 3.458811
#> [79,] 3.531154 3.520305 3.492452 3.483883 3.496791 3.497872 3.469823
#> [80,] 3.548951 3.540946 3.537673 3.529833 3.569612 3.590835 3.528992
#> [81,] 3.430297 3.436254 3.434793 3.423846 3.427134 3.436580 3.496983
#> [82,] 3.518367 3.546952 3.554404 3.566290 3.542905 3.572230 3.465579
#> [83,] 3.641664 3.620972 3.622937 3.613086 3.596059 3.644268 3.701170
#> [84,] 3.573877 3.582581 3.566161 3.540749 3.527827 3.506276 3.523236
#> [85,] 3.534341 3.552258 3.527131 3.536389 3.575518 3.541205 3.544302
#> [86,] 3.557147 3.570561 3.567646 3.559453 3.566055 3.574008 3.506223
#> [87,] 3.619995 3.604493 3.604941 3.612196 3.582978 3.568372 3.613629
#> [88,] 3.543312 3.547323 3.550345 3.559110 3.549203 3.504269 3.507975
#> [89,] 3.610753 3.598837 3.604307 3.603916 3.593153 3.645359 3.693887
#> [90,] 3.568488 3.569566 3.567333 3.534067 3.516229 3.477235 3.524836
#> [91,] 3.415650 3.429583 3.416788 3.439684 3.463072 3.462385 3.401245
#> [92,] 3.506386 3.525968 3.532192 3.517246 3.543946 3.553489 3.506093
#> [93,] 3.458539 3.457662 3.463705 3.459186 3.455204 3.479872 3.476516
#> [94,] 3.593504 3.604020 3.549004 3.551682 3.587204 3.569907 3.555508
#> [95,] 3.571756 3.575663 3.595824 3.588690 3.568763 3.569601 3.601021
#> [96,] 3.422565 3.441104 3.419887 3.450796 3.459347 3.458814 3.469709
#> [97,] 3.555452 3.543470 3.516661 3.516062 3.528663 3.567465 3.501219
#> [98,] 3.534641 3.537986 3.491953 3.507671 3.497333 3.465133 3.474629
#> [99,] 3.502278 3.467269 3.449484 3.462237 3.456829 3.436931 3.491394
#> [100,] 3.542257 3.540657 3.530272 3.540752 3.549235 3.548900 3.533445