Since I started to use rvtests I focused on the Burden test "exactCMC" and on the related single test "exact".
The following two questions for you are related to these tests:
1) the first one concerns the exact meaning of the columns "PvalueTwoSide", "PvalueLess" and "PvalueGreater". In particular the last two columns could be interpreted as the p-values related to the confidence interval of the Odd Ratio of the Fisher test?
2) While performing the single test "exact" I usually obtain that some variants in the output are repeated. In the vcf file that I give as input I did not find these repetitions. So I don't understand how and why they emerge in the output file. I have attached an example to clarify this point.
Hi Xiaowei,
Since I started to use rvtests I focused on the Burden test "exactCMC" and on the related single test "exact". The following two questions for you are related to these tests:
1) the first one concerns the exact meaning of the columns "PvalueTwoSide", "PvalueLess" and "PvalueGreater". In particular the last two columns could be interpreted as the p-values related to the confidence interval of the Odd Ratio of the Fisher test? 2) While performing the single test "exact" I usually obtain that some variants in the output are repeated. In the vcf file that I give as input I did not find these repetitions. So I don't understand how and why they emerge in the output file. I have attached an example to clarify this point.
Thank you in advance!
Margherita
Gene | CHROM | POS | REF | ALT | N_INFORMATIVE | N00 | N01 | N10 | N11 | CtrlAF | CaseAF | PvalueTwoSide | PvalueLess | PvalueGreater GRIN2A | 16 | 10031388 | G | C | 80 | 90 | 68 | 0 | 2 | 0 | 0.0285714 | 0.189858 | 1 | 0.189858 GRIN2A | 16 | 10031388 | G | C | 80 | 90 | 68 | 0 | 2 | 0 | 0.0285714 | 0.189858 | 1 | 0.189858 GRIN2A | 16 | 10031388 | G | C | 80 | 90 | 68 | 0 | 2 | 0 | 0.0285714 | 0.189858 | 1 | 0.189858 FAM168B | 2 | 131809197 | C | T | 80 | 90 | 62 | 0 | 8 | 0 | 0.114286 | 0.00105868 | 1 | 0.00105868 FAM168B | 2 | 131809197 | C | T | 80 | 90 | 62 | 0 | 8 | 0 | 0.114286 | 0.00105868 | 1 | 0.00105868 FAM168B | 2 | 131809197 | C | T | 80 | 90 | 62 | 0 | 8 | 0 | 0.114286 | 0.00105868 | 1 | 0.00105868 FAM168B | 2 | 131809197 | C | T | 80 | 90 | 62 | 0 | 8 | 0 | 0.114286 | 0.00105868 | 1 | 0.00105868 FAM168B | 2 | 131809197 | C | T | 80 | 90 | 62 | 0 | 8 | 0 | 0.114286 | 0.00105868 | 1 | 0.00105868 FAM168B | 2 | 131809197 | C | T | 80 | 90 | 62 | 0 | 8 | 0 | 0.114286 | 0.00105868 | 1 | 0.00105868 FAM168B | 2 | 131809197 | C | T | 80 | 90 | 62 | 0 | 8 | 0 | 0.114286 | 0.00105868 | 1 | 0.00105868