filter_snps: Filter SNPs

In RajLabMSSM/echodata: echoverse module: Fine-mapping data access and formatting

Filter SNPs

Description

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

Usage

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)

RajLabMSSM/echodata documentation built on Nov. 21, 2023, 8 a.m.