LDlinkR

LDlinkR computes linkage disequilibrium (LD) statistics from 1000 Genomes Project germline variant data for population-specific analyses in human genetics and evolutionary studies.

Key Features:

• Rapid calculation: Performs efficient LD computations that reduce time compared with manual web-based queries.
• Programmatic batch querying: Accepts large lists of genetic variants and processes them programmatically to avoid repetitive manual requests.
• Integration with LDlink and 1000 Genomes Project: Interfaces with the LDlink suite and uses 1000 Genomes Project population groups for population-specific analyses.
• Data outputs: Produces pairwise LD estimates and can generate tables and plots of LD statistics for downstream analysis.

Scientific Applications:

• Population genetics: Provides population-specific LD estimates to study genetic structure and variation across human populations.
• Genomic medicine: Supports mapping of genomic regions associated with disease susceptibility through LD-based analyses.
• Evolutionary biology: Enables analysis of LD patterns to investigate evolutionary histories and demographic processes.

Methodology:

Queries 1000 Genomes Project germline variant data for specified population groups and programmatically computes pairwise LD statistics for input variant lists, returning detailed LD tables and plots.