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June 22, 2015 20:29
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associate dunn.test p-values, adjusted p-values with group-group tests
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> 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 | |
> |
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