Model Comparison of CpG Filtering and SNP Polarization Methods in Primates

Summary statistics from 4-mer regression models for three primate species, comparing combinations of CpG filtering and SNP polarization methods. The dataset, created by Sheel Chandra and last updated in June 2026, includes the proportion of variance explained and counts of CpG sites and SNPs. It is a small dataset, 9.7 KB in size, shared under a CC-BY-4.0 license.

Use Cases

• Benchmarking CpG filtering methods based on the intersected reference genome and hard-masked reference genome approaches described.
• Comparing SNP polarization techniques using minor allele frequency (MAF) versus ancestral allele (ANC) methods.
• Evaluating model performance across species based on the proportion of variance explained metric provided.
• Analyzing the relationship between CpG site counts and SNP counts after excluding genic and conserved regions.

Strengths

• Includes results for three distinct primate species, allowing for cross-species comparison.
• Provides a direct comparison of two CpG filtering methods and two SNP polarization methods.
• The proportion of variance explained is calculated using a defined formula (difference between null and residual deviance, divided by null deviance).
• Released under a permissive CC-BY-4.0 license.

Limitations

• Row count is unknown, which may limit suitability assessment.
• Column-level documentation is absent; field semantics must be inferred after download.
• The dataset's 9.7 KB size indicates a very limited scope, likely containing only summary results.

Provenance

Source

figshare

Collection Method

Likely derived from genomic analysis of three primate species, involving regression modeling and SNP inference.

Freshness

Last updated 2026-06-01 17:47:58; freshness should be verified.