associate dunn.test p-values, adjusted p-values with group-group tests

r-script-output.R

> band_class_pvals
                test_name   upper     Pvalue region
   1: unannotated to CTCF   10000 13.0077750      1
   2: unannotated to CTCF   20000  0.0000000      1
   3: unannotated to CTCF   30000  0.9957614      1
   4: unannotated to CTCF   40000  0.2821918      1
   5: unannotated to CTCF   50000  0.3926610      1
  ---                                              
1996:      DNase to DNase 1960000  0.0000000     20
1997:      DNase to DNase 1970000  0.0000000     20
1998:      DNase to DNase 1980000  0.0000000     20
1999:      DNase to DNase 1990000  0.0000000     20
2000:      DNase to DNase 2000000  0.0000000     20
> region_one <- band_class_pvals[region == 1]
> dunn_result = dunn.test(region_one[,.(Pvalue)],region_one[,.(test_name)], method = "bh")
  Kruskal-Wallis rank sum test

data: x and group
Kruskal-Wallis chi-squared = 0, df = 0, p-value = 1

Error in Psort[1, i] : subscript out of bounds
In addition: Warning message:
In matrix(c(P, 1:m, rep(0, m)), 3, m, byrow = TRUE) :
  data length exceeds size of matrix
> region_one[,.(Pvalue)]
          Pvalue
  1:  13.0077750
  2:   0.0000000
  3:   0.9957614
  4:   0.2821918
  5:   0.3926610
  6:   0.4952049
  7:   0.4279606
  8:   1.6523151
  9:   1.6442252
 10:   2.8602400
 11: 255.0000000
 12:   3.7235377
 13:   2.2816602
 14:   3.1144581
 15:   0.5504734
 16:   3.2105646
 17:   2.9425885
 18:   3.3498122
 19:   2.7327976
 20:   1.8982847
 21:   0.1149122
 22:   0.0000000
 23:   0.0000000
 24:   0.0000000
 25:   0.0000000
 26:   0.0000000
 27:   0.0000000
 28:   0.0000000
 29:   0.0000000
 30:   0.0000000
 31:  66.0556312
 32:   3.0522770
 33:   1.2655568
 34:   1.4733414
 35:   0.0000000
 36:   0.0000000
 37:   2.8088404
 38:   8.3639281
 39:  11.3495410
 40:   9.2617886
 41:   9.7473528
 42:   1.4872739
 43:   0.0000000
 44:   0.0000000
 45:   1.7947209
 46:   0.0000000
 47:   3.0969620
 48:   5.6302835
 49:  14.5584748
 50:  33.7298727
 51: 198.8363693
 52:  10.3328100
 53:   5.4530275
 54:   3.8705665
 55:   6.7310807
 56:   3.4883597
 57:  12.6283135
 58:  10.3783273
 59:  14.0566254
 60:  15.9772415
 61:   1.4971105
 62:   0.0000000
 63:   0.0000000
 64:   0.0000000
 65:   0.0000000
 66:   0.0000000
 67:   0.0000000
 68:   0.0000000
 69:   0.0000000
 70:   3.6289607
 71:   3.7655948
 72:   0.0000000
 73:   0.0000000
 74:   0.0000000
 75:   0.0000000
 76:   0.0000000
 77:   0.0000000
 78:   0.0000000
 79:   4.1693302
 80:   0.0000000
 81:   0.0000000
 82:   0.0000000
 83:   0.0000000
 84:   0.0000000
 85:   0.0000000
 86:   0.0000000
 87:   0.0000000
 88:   0.0000000
 89:   0.0000000
 90:   0.0000000
 91:   0.7103008
 92:   0.0000000
 93:   0.0000000
 94:   0.0000000
 95:   0.0000000
 96:   0.0000000
 97:   0.0000000
 98:   0.0000000
 99:   0.0000000
100:   0.0000000
          Pvalue
> dunn_result = dunn.test(region_one[,Pvalue],region_one[,test_name], method = "bh")
  Kruskal-Wallis rank sum test

data: x and group
Kruskal-Wallis chi-squared = 61.8739, df = 9, p-value = 0


                           Comparison of x by group                            
                             (Benjamini-Hochberg)                              
Col Mean-|
Row Mean |   unannota   unannota   unannota   unannota   CTCF to    CTCF to 
---------+------------------------------------------------------------------
unannota |   1.190609
         |     0.1754
         |
unannota |  -2.529530  -3.720140
         |    0.0128*    0.0006*
         |
unannota |   0.704478  -0.486131   3.234009
         |     0.3093     0.3712    0.0027*
         |
CTCF to  |   0.428454  -0.762155   2.957985  -0.276023
         |     0.3759     0.3136    0.0046*     0.4294
         |
CTCF to  |   2.459494   1.268885   4.989025   1.755016   2.031040
         |    0.0142*     0.1586    0.0000*     0.0637     0.0380
         |
DNase-K2 |  -2.006321  -3.196931   0.523209  -2.710800  -2.434776  -4.465816
         |     0.0388    0.0028*     0.3654    0.0084*    0.0146*    0.0000*
         |
CTCF to  |  -1.825052  -3.015662   0.704478  -2.529530  -2.253507  -4.284547
         |     0.0567    0.0041*     0.3184    0.0135*    0.0227*    0.0001*
         |
DNase to |  -2.739638  -3.930248  -0.210107  -3.444116  -3.168093  -5.199133
         |    0.0081*    0.0003*     0.4362    0.0014*    0.0027*    0.0000*
         |
DNase-K2 |  -2.480093  -3.670703   0.049437  -3.184572  -2.908548  -4.939588
         |    0.0141*    0.0007*     0.4803    0.0027*    0.0051*    0.0000*
Col Mean-|
Row Mean |   DNase-K2   CTCF to    DNase to
---------+---------------------------------
CTCF to  |   0.181269  -2.739638  -3.930248
         |     0.4378    0.0081*    0.0003*
         |
DNase to |  -0.733316  -0.914586  -2.480093
         |     0.3159     0.2616    0.0141*
         |
DNase-K2 |  -0.473772  -0.655041   0.259544
         |     0.3667     0.3203     0.4260

> dunn_result$P.adjusted
 [1] 1.753551e-01 1.284920e-02 6.400024e-04 3.093010e-01 3.711754e-01 2.746473e-03 3.759300e-01 3.135709e-01 4.644849e-03 4.294371e-01 1.422947e-02 1.586498e-01
[13] 6.827010e-06 6.368824e-02 3.802582e-02 3.878821e-02 2.841094e-03 3.653688e-01 8.390133e-03 1.457706e-02 4.486719e-05 5.666094e-02 4.121016e-03 3.183981e-01
[25] 1.352548e-02 2.271299e-02 8.240022e-05 4.378071e-01 8.140606e-03 3.182182e-04 4.361775e-01 1.432320e-03 2.655733e-03 4.504945e-06 3.159309e-01 2.615872e-01
[37] 1.407298e-02 6.802980e-04 4.802855e-01 2.718152e-03 5.106246e-03 5.871563e-06 3.667283e-01 3.202757e-01 4.260080e-01
>