Effective sample size for continuous trait

[Thanh Le]

My summary statistics dataset for a continuous trait has SNP-specific sample size, which is the number of individuals after QC being tested for association at a specific variant. The QC procedure removes samples with low call rate, extreme heterozygosity, sex mismatch, and duplicates.

It's stated on GenomicSEM wiki that the total sample size should be used for continuous trait. Should this be the SNP-specific sample size mentioned above?

Best regards,

Thanh Le

[Elliot Tucker-Drob]

if you list the N as NA and include a column with SNP-specific N, you should be good to go. here is a section from the wiki:

#list the sample sizes. All but PTSD have SNP-specific sum of effective sample sizes so only its
#sample size is listed here
N=c(NA,5831.346,NA,NA)

Your subject line refers to effective sample size. We use that term with respect to binary phenotypes, where it refers to the sample size of an equivalently powered case control gwas with balanced numbers of cases and controls. We use the term N_hat to refer to the predicted sample size based on the (standardized) beta and SE. In the common factor gwas section of the wiki, see the subsection titled Calculating sample size for factors. Note that we provide further detail on this supplementary section S6 of https://www.biologicalpsychiatryjournal.com/article/S0006-3223(22)01316-6/abstract

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