Filter SNPs

Filter SNPs by MAF, window size, min/max position, maximum number of SNPs, or gene coordinates. You can also explicitly remove certain variants.

filter_snps(
  dat,
  bp_distance = 5e+05,
  remove_variants = FALSE,
  min_POS = NA,
  max_POS = NA,
  max_snps = NULL,
  min_MAF = NULL,
  trim_gene_limits = FALSE,
  verbose = TRUE
)

Arguments

dat

Fine-mapping results data.

bp_distance

Distance around the lead SNP to include.

remove_variants

A list of SNP RSIDs to remove.

min_POS

Minimum genomic position to include.

max_POS

Maximum genomic position to include.

max_snps

Maximum number of SNPs to include.

min_MAF

Minimum Minor Allele Frequency (MAF) of SNPs to include.

trim_gene_limits

If a gene name is supplied to this argument (e.g. trim_gene_limits="BST"), only SNPs within the gene body will be included.

verbose

Print messages.

See also

Other SNP filters: gene_trimmer(), limit_snps()

Examples

dat <- echodata::filter_snps(dat = echodata::BST1)
#> FILTER:: Filtering by SNP features.
#> + FILTER:: Post-filtered data: 2913 x 26