SEQanswers

SEQanswers (http://seqanswers.com/forums/index.php)
-   Bioinformatics (http://seqanswers.com/forums/forumdisplay.php?f=18)
-   -   Stats help, interpreting the output of bedtools fisher (http://seqanswers.com/forums/showthread.php?t=67731)

biocomputer 04-20-2016 03:41 PM

Stats help, interpreting the output of bedtools fisher
 
Forgive me if this is trivial, I want to make sure I understand the output of bedtools fisher. I've used it to compare several sets of intervals in the human genome and want to say whether two sets of intervals have a statistically significant overlap or not. Here are the abbreviated outputs from 6 tests (I can give the full outputs if needed):

Code:

Test  left    right  two-tail        ratio
1:    0      1      0      3.655
2:    1      1.3018e-39      2.5115e-39      1.180
3:    1      4.9869e-47      9.3199e-47      1.198
4:    1      3.7421e-45      6.909e-45      1.194
5:    0.71641        0.40143        0.61502        1.123
6:    0.63306        0.49828        0.86348        1.040

Is it correct that: a small left p-value indicates the intervals overlap significantly more than expected (test #1 above), a small right p-value indicates the intervals overlap significantly less than expected (tests 2,3,4), and if neither the left or right p-values are small (tests 5,6) the intervals overlap "randomly" (not sure what the correct term is, basically they don't overlap more or less than would be expected)? Also I don't understand how to interpret the two-tail p-value and ratio for these tests. Thank you to anyone who can help clarify this for me.


All times are GMT -8. The time now is 04:56 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.