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)
#> FILTER:: Filtering by SNP features.
#> + FILTER:: Post-filtered data: 2913 x 26