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perslab / CELLECT

CELLECT (CELL-type Expression-specific integration for Complex Traits)
GNU General Public License v3.0
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LD-based windows SNP loss #20

Closed Tobi1kenobi closed 4 years ago

Tobi1kenobi commented 5 years ago

Problem

LD-based gene windows using SNPsnap data results in a roughly 15% loss of SNPs and performance is impacted as a a result.

Solution

Recalculate LD between CELLECT-LDSC's HapMap3 input SNPs and Ensembl human genes then replace SNPsnap data.