Identifies independent significant loci using window-based clumping, optionally annotates with nearest gene, and returns a publication-ready table.
Usage
top_hits(
data,
p_threshold = 5e-08,
clump_window = 1e+06,
genes = NULL,
max_gene_distance = 5e+05,
n = 20
)Arguments
- data
A
gwas_dataobject or data.frame.- p_threshold
Significance threshold for lead SNPs.
- clump_window
Window size in bp for clumping. Only the most significant SNP within each window is retained.
- genes
Optional gene annotation data.frame (chr, start, end, gene). If provided, nearest gene is added.
- max_gene_distance
Maximum distance to assign a gene.
- n
Maximum number of hits to return.
Value
A data.frame with columns: SNP, CHR, BP, P, BETA, SE, nearest_gene (if genes provided), gene_distance, cytoband.
Examples
data(example_gwas)
top_hits(example_gwas, p_threshold = 0.001, n = 10)
#> === Top 10 GWAS Hits ===
#>
#> SNP CHR BP P BETA cytoband
#> rs4551863 10 12347484 1.19e-14 -0.65050 10p2
#> rs6815318 5 8647048 1.67e-14 0.22025 5p1
#> rs7084233 9 67050634 2.21e-14 0.09187 9q7
#> rs3834775 11 55974589 3.20e-14 -0.44376 11q6
#> rs7664467 1 243745976 1.13e-13 0.27479 1q25
#> rs5643433 12 25442148 1.27e-13 0.37069 12p3
#> rs8682426 8 82835070 6.14e-12 0.31901 8q9
#> rs5807931 1 32792647 2.75e-11 0.14800 1p4
#> rs4355535 14 80736074 7.20e-11 -0.02754 14q9
#> rs8870315 2 123129235 7.36e-11 0.09318 2q13