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Find the nearest gene for variants

Source: R/annotate.R
find_nearest_gene.Rd

Find the nearest gene for variants

Usage

find_nearest_gene(x, ...)

# S3 method for class 'GWASFormatter'
find_nearest_gene(x, threshold = 1e+05, ...)

# S3 method for class 'tbl_df'
find_nearest_gene(
  x,
  threshold = 1e+05,
  chrom_col = "CHROM",
  pos_col = "POS",
  id_col = "ID",
  ...
)

Arguments

x

A gwas object or tibble containing variant data.

...

Additional arguments passed to methods.

threshold

The distance threshold to consider a gene as nearest. Default is 1e5.

chrom_col

Name of the column containing chromosome information. Default is "CHROM".

pos_col

Name of the column containing position information. Default is "POS".

id_col

Name of the column containing variant IDs. Default is "ID".

Value

The input object with gene annotations added.

Methods (by class)

  • find_nearest_gene(GWASFormatter): Find the nearest gene for each variant in a gwas object

  • find_nearest_gene(tbl_df): Find the nearest gene for each variant in a tibble