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UMAP

Definition
AI-generated

UMAP (Uniform Manifold Approximation and Projection) is a nonlinear dimension-reduction method.

Topics
Machine learning concepts
Related
Ancestry Multidimensional Scaling (MDS) Principal Component Analysis (PCA)

Why it matters in GWAS

It can reveal fine-scale geographic or subgroup structure not obvious in linear PCs alone but is supplementary to, not a substitute for, standard PC-based association adjustment.

Example usage

"We ran UMAP on the first 20 PCs to visualize subclusters within the nominally homogeneous cohort."

Ancestry Multidimensional Scaling (MDS) Principal Component Analysis (PCA) SCANPY Single-Cell Sequencing Trajectory Inference
Related-term network

Click any node to open that term page.

Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • Diaz-Papkovich A, Anderson-Trocmé L, Gravel S. (2021). A review of UMAP in population genetics. J Hum Genet.
  • GWASTutorial: PCA-UMAP.
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