SFDR (Stratified False Discovery Rate control) is a program to compute FDR q-values of genome-wide SNP association analysis within each stratum. Especialy the SFDR program is taylored to directly use genome-wide linkage scan results to assign strata. Weighted FDR q-values can be also computed as an alternative to SFDR. To understand the details of FDR, SFDR and WFDR control methods
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Sun, L., Craiu, R.V., Paterson, A.D. & Bull, S.B.
Stratified false discovery control for large-scale hypothesis testing with application to genome-wide association studies.
Genet. Epidemiol. 30, 519-530 (2006)