cl_interval.Rdcl_interval is a function that allows the user to obtain a confidence
interval for the adjusted association estimates of significant SNPs, which
have been obtained through the implementation of
conditional_likelihood. This function produces one confidence
interval for each significant SNP, based on the approach suggested in
Ghosh et
al. (2008). Note that in order for an appropriate confidence interval to be
outputted for each significant SNP, the absolute value of the largest
\(z\)-statistic in the data set must be less than 150.
cl_interval(summary_data, alpha = 5e-08, conf_level = 0.95)A data frame containing summary statistics from the
discovery GWAS. It must have three columns with column names rsid,
beta and se, respectively, and columns beta and
se must contain numerical values. Each row must correspond to a
unique SNP, identified by rsid.
A numerical value which specifies the desired genome-wide
significance threshold. The default is given as 5e-8.
A numerical value between 0 and 1 which determines the
confidence interval to be computed. The default setting is 0.95
which results in the calculation of a 95% confidence interval for the
adjusted association estimate for each SNP.
A data frame which combines the output of
conditional_likelihood with two additional columns, namely
lower and upper, containing the lower and upper bounds of the
required confidence interval for each significant SNP, respectively.
However, if no SNPs are detected as significant in the data set,
cl_interval returns a warning message: "WARNING: There are no
significant SNPs at this threshold."
Ghosh, A., Zou, F., & Wright, F. A. (2008). Estimating odds ratios in genome scans: an approximate conditional likelihood approach. American journal of human genetics, 82(5), 1064\(-\)1074. doi:10.1016/j.ajhg.2008.03.002
conditional_likelihood for details on operation of
conditional likelihood methods with summary statistics from discovery GWAS.
https://amandaforde.github.io/winnerscurse/articles/standard_errors_confidence_intervals.html
for illustration of the use of cl_interval with a toy data set and
further information regarding the manner in which the confidence interval
is computed.