Compute in Depth

Score harmonization details

Explain variant matching, allele handling, and variant-fate outputs for debugging and auditability.

Quality-control controls

Show practical usage of minor.allele.freq.threshold and model.filter for stable scoring.

Population structure and relatedness

In-sample PCA

Compute in-sample PCs and store in data$obsm for confounder adjustment.

Projected PCA (reference projection)

Cover reference.panel projection mode explicitly, including when projection is preferred over in-sample PCA.

Kinship

Compute relatedness matrices and connect them to downstream modeling decisions.

Compute troubleshooting

Provide quick diagnostics for build mismatch, low match rates, and QC-driven score loss.