Changes

For CPD we will consider the binned responses to be on a quantitative scale from 1-4 (see above under the CPD phenotype description). '''CPD therefore will not require transformation''' prior to covariate correction.

For CPD we will consider the binned responses to be on a quantitative scale from 1-4 (see above under the CPD phenotype description). '''CPD therefore will not require transformation''' prior to covariate correction.

For all other phenotypes (Pack Years, Smoking Initiation, Age of Initiation, Drinks Per Week) please '''left-anchor''' the distribution at 1 and '''log-transform it'''. (Left-anchoring, such that no value is less than 1, prevents the log-transform from returning nonsensical values like negative infinity). Then apply the covariate correction to the transformed phenotypes.

For the other four quantitative phenotypes (Pack Years, Age of Initiation, Drinks Per Week) please '''left-anchor''' the distribution at 1 and '''log-transform it'''. Left-anchoring, such that no value is less than 1, prevents the log-transform from returning nonsensical values like negative infinity. Then apply the covariate correction to the transformed phenotypes. This step is unnecessary for the binary smoking initiation phenotype

Appropriate covariates can often be study-specific.  We will depend on local investigators to determine the most appropriate covariates.  We list here some covariates that will likely be necessary.

Appropriate covariates can often be study-specific.  We will depend on local investigators to determine the most appropriate covariates.  We list here some covariates that will likely be necessary.