7 Linear Regression

It is possible to use a quantitative trait for the phenotype instead of the case-control status. To do this use the -linear option. For example:

./snipsnip -linear -o myresults.dat mydata.bed

In this case the phenotype column in the .fam file should contain the phenotype of interest. The missing quantitative trait value is set by default to -9. This can be changed with the -mqtv option. For example, to set the missing quantitative trait value to 0:

./snipsnip -linear -mqtv 0 -o myresults.dat mydata.bed

When using linear regression the partner SNP is chosen in exactly the same manner as before and the same equivilent models are compared, but this time using an F-test.

Again, for more details concerning the methodology, please read the accompanying manuscript Howey and Cordell (2014).