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Compute p-value for perplexity via permutation

Source: R/calc_metrics.R
perplexityPermute.Rd

Compute p-value for perplexity via permutation

Usage

perplexityPermute(spe, pm = NA, pm_cols = NA, n_perm = 1000)

Arguments

spe

A SpatialExperiment object.

pm

Optional. The probability matrix.

pm_cols

The colnames of probability matrix. This is requires for SpatialExperiment input. Assuming that the probability is stored in the colData.

n_perm

Integer number. The number of permutation. 1000 by default.

Value

A SpatialExperiment object. Calculated P-value and adjusted P-value are saved as columns in the colData of the SpatialExperiment object. P-value and adjusted P-value are calculated based on permutation test and Benjamini Hochberg correction.

Examples


data("spe_test")

spe <- readHoodData(spe, anno_col = "celltypes")

fnc <- findNearCells(spe, k = 100)

pm <- scanHoods(fnc$distance)
#> Tau is set to: 22747.4

pm2 <- mergeByGroup(pm, fnc$cells)

spe <- mergeHoodSpe(spe, pm2)

spe <- perplexityPermute(spe, pm_cols = colnames(pm2))
#> 
Generating permutation 1 of 1000
Generating permutation 2 of 1000
Generating permutation 3 of 1000
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Generating permutation 10 of 1000
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Generating permutation 40 of 1000
Generating permutation 41 of 1000
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Generating permutation 50 of 1000
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Generating permutation 60 of 1000
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Generating permutation 65 of 1000
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Generating permutation 120 of 1000
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Generating permutation 128 of 1000
Generating permutation 129 of 1000
Generating permutation 130 of 1000
Generating permutation 131 of 1000
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Generating permutation 133 of 1000
Generating permutation 134 of 1000
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Generating permutation 310 of 1000
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Generating permutation 343 of 1000
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Generating permutation 383 of 1000
Generating permutation 384 of 1000
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Generating permutation 388 of 1000
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Generating permutation 398 of 1000
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Generating permutation 438 of 1000
Generating permutation 439 of 1000
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Generating permutation 443 of 1000
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Generating permutation 445 of 1000
Generating permutation 446 of 1000
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Generating permutation 448 of 1000
Generating permutation 449 of 1000
Generating permutation 450 of 1000
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Generating permutation 453 of 1000
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Generating permutation 468 of 1000
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Generating permutation 470 of 1000
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Generating permutation 480 of 1000
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Generating permutation 486 of 1000
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Generating permutation 493 of 1000
Generating permutation 494 of 1000
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Generating permutation 500 of 1000
Generating permutation 501 of 1000
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Generating permutation 508 of 1000
Generating permutation 509 of 1000
Generating permutation 510 of 1000
Generating permutation 511 of 1000
Generating permutation 512 of 1000
Generating permutation 513 of 1000
Generating permutation 514 of 1000
Generating permutation 515 of 1000
Generating permutation 516 of 1000
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Generating permutation 533 of 1000
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Generating permutation 536 of 1000
Generating permutation 537 of 1000
Generating permutation 538 of 1000
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Generating permutation 541 of 1000
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Generating permutation 553 of 1000
Generating permutation 554 of 1000
Generating permutation 555 of 1000
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Generating permutation 557 of 1000
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Generating permutation 566 of 1000
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Generating permutation 568 of 1000
Generating permutation 569 of 1000
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Generating permutation 571 of 1000
Generating permutation 572 of 1000
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Generating permutation 576 of 1000
Generating permutation 577 of 1000
Generating permutation 578 of 1000
Generating permutation 579 of 1000
Generating permutation 580 of 1000
Generating permutation 581 of 1000
Generating permutation 582 of 1000
Generating permutation 583 of 1000
Generating permutation 584 of 1000
Generating permutation 585 of 1000
Generating permutation 586 of 1000
Generating permutation 587 of 1000
Generating permutation 588 of 1000
Generating permutation 589 of 1000
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Generating permutation 593 of 1000
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Generating permutation 596 of 1000
Generating permutation 597 of 1000
Generating permutation 598 of 1000
Generating permutation 599 of 1000
Generating permutation 600 of 1000
Generating permutation 601 of 1000
Generating permutation 602 of 1000
Generating permutation 603 of 1000
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Generating permutation 606 of 1000
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Generating permutation 610 of 1000
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Generating permutation 625 of 1000
Generating permutation 626 of 1000
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Generating permutation 628 of 1000
Generating permutation 629 of 1000
Generating permutation 630 of 1000
Generating permutation 631 of 1000
Generating permutation 632 of 1000
Generating permutation 633 of 1000
Generating permutation 634 of 1000
Generating permutation 635 of 1000
Generating permutation 636 of 1000
Generating permutation 637 of 1000
Generating permutation 638 of 1000
Generating permutation 639 of 1000
Generating permutation 640 of 1000
Generating permutation 641 of 1000
Generating permutation 642 of 1000
Generating permutation 643 of 1000
Generating permutation 644 of 1000
Generating permutation 645 of 1000
Generating permutation 646 of 1000
Generating permutation 647 of 1000
Generating permutation 648 of 1000
Generating permutation 649 of 1000
Generating permutation 650 of 1000
Generating permutation 651 of 1000
Generating permutation 652 of 1000
Generating permutation 653 of 1000
Generating permutation 654 of 1000
Generating permutation 655 of 1000
Generating permutation 656 of 1000
Generating permutation 657 of 1000
Generating permutation 658 of 1000
Generating permutation 659 of 1000
Generating permutation 660 of 1000
Generating permutation 661 of 1000
Generating permutation 662 of 1000
Generating permutation 663 of 1000
Generating permutation 664 of 1000
Generating permutation 665 of 1000
Generating permutation 666 of 1000
Generating permutation 667 of 1000
Generating permutation 668 of 1000
Generating permutation 669 of 1000
Generating permutation 670 of 1000
Generating permutation 671 of 1000
Generating permutation 672 of 1000
Generating permutation 673 of 1000
Generating permutation 674 of 1000
Generating permutation 675 of 1000
Generating permutation 676 of 1000
Generating permutation 677 of 1000
Generating permutation 678 of 1000
Generating permutation 679 of 1000
Generating permutation 680 of 1000
Generating permutation 681 of 1000
Generating permutation 682 of 1000
Generating permutation 683 of 1000
Generating permutation 684 of 1000
Generating permutation 685 of 1000
Generating permutation 686 of 1000
Generating permutation 687 of 1000
Generating permutation 688 of 1000
Generating permutation 689 of 1000
Generating permutation 690 of 1000
Generating permutation 691 of 1000
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Generating permutation 693 of 1000
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Generating permutation 695 of 1000
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Generating permutation 700 of 1000
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Generating permutation 704 of 1000
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Generating permutation 710 of 1000
Generating permutation 711 of 1000
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Generating permutation 713 of 1000
Generating permutation 714 of 1000
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Generating permutation 717 of 1000
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Generating permutation 719 of 1000
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Generating permutation 731 of 1000
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Generating permutation 737 of 1000
Generating permutation 738 of 1000
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Generating permutation 744 of 1000
Generating permutation 745 of 1000
Generating permutation 746 of 1000
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Generating permutation 749 of 1000
Generating permutation 750 of 1000
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Generating permutation 753 of 1000
Generating permutation 754 of 1000
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Generating permutation 756 of 1000
Generating permutation 757 of 1000
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Generating permutation 760 of 1000
Generating permutation 761 of 1000
Generating permutation 762 of 1000
Generating permutation 763 of 1000
Generating permutation 764 of 1000
Generating permutation 765 of 1000
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Generating permutation 767 of 1000
Generating permutation 768 of 1000
Generating permutation 769 of 1000
Generating permutation 770 of 1000
Generating permutation 771 of 1000
Generating permutation 772 of 1000
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Generating permutation 775 of 1000
Generating permutation 776 of 1000
Generating permutation 777 of 1000
Generating permutation 778 of 1000
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Generating permutation 780 of 1000
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Generating permutation 783 of 1000
Generating permutation 784 of 1000
Generating permutation 785 of 1000
Generating permutation 786 of 1000
Generating permutation 787 of 1000
Generating permutation 788 of 1000
Generating permutation 789 of 1000
Generating permutation 790 of 1000
Generating permutation 791 of 1000
Generating permutation 792 of 1000
Generating permutation 793 of 1000
Generating permutation 794 of 1000
Generating permutation 795 of 1000
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Generating permutation 797 of 1000
Generating permutation 798 of 1000
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Generating permutation 810 of 1000
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Generating permutation 844 of 1000
Generating permutation 845 of 1000
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Generating permutation 847 of 1000
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Generating permutation 849 of 1000
Generating permutation 850 of 1000
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Generating permutation 853 of 1000
Generating permutation 854 of 1000
Generating permutation 855 of 1000
Generating permutation 856 of 1000
Generating permutation 857 of 1000
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Generating permutation 859 of 1000
Generating permutation 860 of 1000
Generating permutation 861 of 1000
Generating permutation 862 of 1000
Generating permutation 863 of 1000
Generating permutation 864 of 1000
Generating permutation 865 of 1000
Generating permutation 866 of 1000
Generating permutation 867 of 1000
Generating permutation 868 of 1000
Generating permutation 869 of 1000
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Generating permutation 871 of 1000
Generating permutation 872 of 1000
Generating permutation 873 of 1000
Generating permutation 874 of 1000
Generating permutation 875 of 1000
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Generating permutation 877 of 1000
Generating permutation 878 of 1000
Generating permutation 879 of 1000
Generating permutation 880 of 1000
Generating permutation 881 of 1000
Generating permutation 882 of 1000
Generating permutation 883 of 1000
Generating permutation 884 of 1000
Generating permutation 885 of 1000
Generating permutation 886 of 1000
Generating permutation 887 of 1000
Generating permutation 888 of 1000
Generating permutation 889 of 1000
Generating permutation 890 of 1000
Generating permutation 891 of 1000
Generating permutation 892 of 1000
Generating permutation 893 of 1000
Generating permutation 894 of 1000
Generating permutation 895 of 1000
Generating permutation 896 of 1000
Generating permutation 897 of 1000
Generating permutation 898 of 1000
Generating permutation 899 of 1000
Generating permutation 900 of 1000
Generating permutation 901 of 1000
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Generating permutation 905 of 1000
Generating permutation 906 of 1000
Generating permutation 907 of 1000
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Generating permutation 909 of 1000
Generating permutation 910 of 1000
Generating permutation 911 of 1000
Generating permutation 912 of 1000
Generating permutation 913 of 1000
Generating permutation 914 of 1000
Generating permutation 915 of 1000
Generating permutation 916 of 1000
Generating permutation 917 of 1000
Generating permutation 918 of 1000
Generating permutation 919 of 1000
Generating permutation 920 of 1000
Generating permutation 921 of 1000
Generating permutation 922 of 1000
Generating permutation 923 of 1000
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Generating permutation 925 of 1000
Generating permutation 926 of 1000
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Generating permutation 932 of 1000
Generating permutation 933 of 1000
Generating permutation 934 of 1000
Generating permutation 935 of 1000
Generating permutation 936 of 1000
Generating permutation 937 of 1000
Generating permutation 938 of 1000
Generating permutation 939 of 1000
Generating permutation 940 of 1000
Generating permutation 941 of 1000
Generating permutation 942 of 1000
Generating permutation 943 of 1000
Generating permutation 944 of 1000
Generating permutation 945 of 1000
Generating permutation 946 of 1000
Generating permutation 947 of 1000
Generating permutation 948 of 1000
Generating permutation 949 of 1000
Generating permutation 950 of 1000
Generating permutation 951 of 1000
Generating permutation 952 of 1000
Generating permutation 953 of 1000
Generating permutation 954 of 1000
Generating permutation 955 of 1000
Generating permutation 956 of 1000
Generating permutation 957 of 1000
Generating permutation 958 of 1000
Generating permutation 959 of 1000
Generating permutation 960 of 1000
Generating permutation 961 of 1000
Generating permutation 962 of 1000
Generating permutation 963 of 1000
Generating permutation 964 of 1000
Generating permutation 965 of 1000
Generating permutation 966 of 1000
Generating permutation 967 of 1000
Generating permutation 968 of 1000
Generating permutation 969 of 1000
Generating permutation 970 of 1000
Generating permutation 971 of 1000
Generating permutation 972 of 1000
Generating permutation 973 of 1000
Generating permutation 974 of 1000
Generating permutation 975 of 1000
Generating permutation 976 of 1000
Generating permutation 977 of 1000
Generating permutation 978 of 1000
Generating permutation 979 of 1000
Generating permutation 980 of 1000
Generating permutation 981 of 1000
Generating permutation 982 of 1000
Generating permutation 983 of 1000
Generating permutation 984 of 1000
Generating permutation 985 of 1000
Generating permutation 986 of 1000
Generating permutation 987 of 1000
Generating permutation 988 of 1000
Generating permutation 989 of 1000
Generating permutation 990 of 1000
Generating permutation 991 of 1000
Generating permutation 992 of 1000
Generating permutation 993 of 1000
Generating permutation 994 of 1000
Generating permutation 995 of 1000
Generating permutation 996 of 1000
Generating permutation 997 of 1000
Generating permutation 998 of 1000
Generating permutation 999 of 1000
Generating permutation 1000 of 1000