A useful statistic is to normalize the estimate of sigma from estimateSlope, the dispersion, with respect to typical mediated effect sizes. This helps in particular to compare sigma across different GWAS traits, which may have different scale.

normalizedAllelicSpread(fit)

Arguments

fit

a list output by estimateSlope

Value

the normalized allelic spread, a numeric

Details

We define the normalized allelic spread as an estimate of sigma divided by something called the "mean mediated effect". The mean mediated effect is defined as the mean QTL effect size multiplied by the estimate of the slope. So in the plotMrlocus plot, the mean mediated effect is found by taking the mean among the spread of points on the x-axis, then going up to the linear trend. This function outputs the normalized allelic spread which is again: sigma / mean mediated effect.