I have output from plink haplotype analysis, however I do not have the raw data. Here, is the output for Haplotype-based association tests with GLMs:
SNP1 SNP2 HAPLOTYPE F OR STAT P
rs1 rs2 22 0.00992 4.23 61.5 4.43E-15
rs1 rs2 12 0.038 1.02 0.217 0.642
rs1 rs2 21 0.00015 5.22E-10 453 1.77E-100
rs1 rs2 11 0.952 0.762 22.9 1.73E-06
Here is the explanation for each column from plink:
SNP1 SNP ID of left-most (5') SNP
SNP2 SNP ID of left-most (3') SNP
HAPLOTYPE Haplotype
F Frequency in sample
OR Estimated odds ratio
STAT Test statistic (T from Wald test)
P Asymptotic p-value
Question: based on above output, is it possible to calculate OR
95% confidence intervals?
Best Answer
For the calculation of confidence intervals you'll need standard errors for the effects, but those are not available in the output. However, the standard errors can be estimated from the Wald statistics and odds ratios.
The calculation goes as follows:
So, your odds ratio for the first row of the table is 4.23 and it's 95% confidence interval is 2.949-6.065. Because the confidence interval does not include one, the results is statistically significant. The results are subject to error due to rounding of the output from PLINK.
This calculation can be achieved in, e.g., Excel, but below is also an R function that does the same thing (just in case you also use R).