21 Statistics: Simes method
Simes method lets you combine dependent p-values into one. The function takes three arguments: a dataframe, the columns identifying the rows to merge and the column containing the p-values.
import numpy as np
import pyranges as pr
gr = pr.random()
gr.P = np.random.random(len(gr))
gr.Cluster = np.random.randint(20, size=len(gr))
print(gr)## +--------------+-----------+-----------+--------------+-------+
## | Chromosome | Start | End | Strand | +2 |
## | (category) | (int32) | (int32) | (category) | ... |
## |--------------+-----------+-----------+--------------+-------|
## | chr1 | 27293486 | 27293586 | + | ... |
## | chr1 | 127383507 | 127383607 | + | ... |
## | chr1 | 225512616 | 225512716 | + | ... |
## | chr1 | 176131037 | 176131137 | + | ... |
## | ... | ... | ... | ... | ... |
## | chrY | 38491895 | 38491995 | - | ... |
## | chrY | 26337904 | 26338004 | - | ... |
## | chrY | 40786076 | 40786176 | - | ... |
## | chrY | 26500663 | 26500763 | - | ... |
## +--------------+-----------+-----------+--------------+-------+
## Stranded PyRanges object has 1,000 rows and 6 columns from 24 chromosomes.
## For printing, the PyRanges was sorted on Chromosome and Strand.
## 2 hidden columns: P, Clusterprint(pr.stats.simes(gr.df, "Cluster", "P"))## Cluster Simes
## 0 0 0.294263
## 1 1 0.194612
## 2 2 0.138653
## 3 3 0.242226
## 4 4 0.547232
## 5 5 0.831406
## 6 6 0.474479
## 7 7 0.862408
## 8 8 0.551776
## 9 9 0.114838
## 10 10 0.426132
## 11 11 0.055800
## 12 12 0.540235
## 13 13 0.880630
## 14 14 0.492563
## 15 15 0.276158
## 16 16 0.266277
## 17 17 0.667854
## 18 18 0.916523
## 19 19 0.102858print(pr.stats.simes(gr.df, ["Cluster", "Strand"], "P"))## Cluster Strand Simes
## 0 0 + 0.815705
## 1 0 - 0.122011
## 2 1 + 0.647093
## 3 1 - 0.111207
## 4 2 + 0.195375
## 5 2 - 0.043096
## 6 3 + 0.998096
## 7 3 - 0.159766
## 8 4 + 0.539287
## 9 4 - 0.442816
## 10 5 + 0.875164
## 11 5 - 0.423856
## 12 6 + 0.468396
## 13 6 - 0.414288
## 14 7 + 0.934276
## 15 7 - 0.688575
## 16 8 + 0.425527
## 17 8 - 0.523601
## 18 9 + 0.955002
## 19 9 - 0.061247
## 20 10 + 0.213066
## 21 10 - 0.759273
## 22 11 + 0.023644
## 23 11 - 0.211788
## 24 12 + 0.598323
## 25 12 - 0.401967
## 26 13 + 0.607969
## 27 13 - 0.617153
## 28 14 + 0.468841
## 29 14 - 0.321674
## 30 15 + 0.155036
## 31 15 - 0.345685
## 32 16 + 0.313127
## 33 16 - 0.211012
## 34 17 + 0.444700
## 35 17 - 0.594878
## 36 18 + 0.911100
## 37 18 - 0.776099
## 38 19 + 0.370946
## 39 19 - 0.051429