Annotate peaks with nearest gene names

Maps significant SNPs to their nearest gene using a provided gene annotation table. Returns the data with a gene column, or adds gene labels directly to a Manhattan plot.

Usage

annotate_genes(
  data,
  genes,
  p_threshold = 5e-08,
  max_distance = 5e+05,
  top_n = NULL,
  clump_window = 1e+06
)

Arguments

data

A gwas_data object or data.frame.

genes

A data.frame with gene positions. Required columns: chr (integer or "chr1" format), start, end, gene (gene symbol). Optional: strand.

p_threshold

Only annotate SNPs with p < this value.

max_distance

Maximum distance (bp) from SNP to gene midpoint to assign annotation. Default 500kb.

top_n

Annotate only the top N most significant SNPs.

clump_window

Clumping window in bp. Within each window, only the most significant SNP is annotated. Default 1Mb.

Value

A data.frame with added nearest_gene and gene_distance columns.

Examples

data(example_gwas)
genes <- data.frame(
  chr = c(1, 2, 5), start = c(1e6, 50e6, 80e6),
  end = c(1.5e6, 51e6, 82e6), gene = c("GENE_A", "GENE_B", "GENE_C")
)
annotated <- annotate_genes(example_gwas, genes, top_n = 10)
head(annotated[!is.na(annotated$nearest_gene), ])
#> Warning: no non-missing arguments to min; returning Inf
#> A gwas_data object: 0 variants across 0 chromosome
#>   Min p-value: Inf
#>   Lambda GC:   NA
#>   Columns:     CHR, BP, SNP, P, BETA, SE, A1, A2, AF, nearest_gene, gene_distance