Does some standard qc of snp files before gwas. Mainly maf and missing filter. Also filters for single allele snps. Extra calls to plink2 can be included to filter in more ways.
Usage
snp_qc_plink(
genotype.path,
min.maf = 0.05,
max.missing.snp = 0.1,
sample.list.path = NULL,
plink.path = NULL,
out.dir = NULL,
out.prefix = NULL,
extra.options = NULL
)Arguments
- genotype.path
character, path to genotype file, supported types: '.bed', .'vcf', '.vcf.gz'.
- min.maf
numeric, filtering cutoff for minor allele frequency, snps are removed if they have maf less than this value. To ignore set to 0.
- max.missing.snp
numeric, filtering cutoff for missing rate of snps, snps are removed if they have a missing rate higher than this. To ignore set to 1.
- sample.list.path
character, optional, path to a list of samples. Samples in file will be included. Sample filtering happens before other filtering per plink's order of operations.
- plink.path
character, optional, path to plink2 executable. If not provided, will default to option set by set_plink_path.
- out.dir
character, optional, path to output files. If not provided, will default to option set by set_out_dir
- out.prefix
character, optional, prefix for files output.
- extra.options
character, a vector of options to include in call to plink2. Should be a vector with plink2 arguments and their values as separate elements of vector. E.G. c("–max-maf", ".95", "–max-alleles", "2")
Examples
# get some inputs
plink.path <- bigsnpr::download_plink2()
temp.dir <- file.path(tempdir(), "panvar_ex")
dir.create(temp.dir, showWarnings = FALSE)
genotype.path <- system.file("extdata", "Setaria_shattering_example_pruned.bed", package="panvaR")
# run function
snp_qc_plink(
genotype.path = genotype.path,
plink.path = plink.path,
out.dir = temp.dir,
out.prefix = "Example")
#> [1] "/tmp/RtmpPR7nRY/panvar_ex/Example_PlinkQC_maf0.05_missing0.1"
#> PLINK v2.0.0-a.7LM AVX2 Intel (11 Mar 2026) cog-genomics.org/plink/2.0/
#> (C) 2005-2026 Shaun Purcell, Christopher Chang GNU General Public License v3
#> Logging to /tmp/RtmpPR7nRY/panvar_ex/Example_PlinkQC_maf0.05_missing0.1.log.
#> Options in effect:
#> --allow-extra-chr
#> --bfile /home/runner/work/_temp/Library/panvaR/extdata/Setaria_shattering_example_pruned
#> --geno 0.1
#> --maf 0.05
#> --make-bed
#> --out /tmp/RtmpPR7nRY/panvar_ex/Example_PlinkQC_maf0.05_missing0.1
#> --set-all-var-ids @-#
#>
#> Start time: Thu Apr 2 21:27:18 2026
#> 15989 MiB RAM detected, ~14380 available; reserving 7994 MiB for main
#> workspace.
#> Using up to 4 compute threads.
#> 598 samples (0 females, 0 males, 598 ambiguous; 598 founders) loaded from
#> /home/runner/work/_temp/Library/panvaR/extdata/Setaria_shattering_example_pruned.fam.
#> Note: 1 nonstandard chromosome code present.
#> 7715 variants loaded from
#> /home/runner/work/_temp/Library/panvaR/extdata/Setaria_shattering_example_pruned.bim.
#> Note: No phenotype data present.
#> Calculating allele frequencies... 0%done.
#> --geno: 0 variants removed due to missing genotype data.
#> 2354 variants removed due to allele frequency threshold(s)
#> (--maf/--max-maf/--mac/--max-mac).
#> 5361 variants remaining after main filters.
#> Writing /tmp/RtmpPR7nRY/panvar_ex/Example_PlinkQC_maf0.05_missing0.1.fam ...
#> done.
#> Writing /tmp/RtmpPR7nRY/panvar_ex/Example_PlinkQC_maf0.05_missing0.1.bim ...
#> done.
#> Writing /tmp/RtmpPR7nRY/panvar_ex/Example_PlinkQC_maf0.05_missing0.1.bed ...
#> 0%done.
#> End time: Thu Apr 2 21:27:18 2026
#> QC was successful, output stored at /tmp/RtmpPR7nRY/panvar_ex/Example_PlinkQC_maf0.05_missing0.1
#> [1] "/tmp/RtmpPR7nRY/panvar_ex/Example_PlinkQC_maf0.05_missing0.1"
# see what we did
list.files(temp.dir)
#> [1] "Example_PlinkQC_maf0.05_missing0.1.bed"
#> [2] "Example_PlinkQC_maf0.05_missing0.1.bim"
#> [3] "Example_PlinkQC_maf0.05_missing0.1.fam"
#> [4] "Example_PlinkQC_maf0.05_missing0.1.log"
# clean up
unlink(temp.dir, recursive = TRUE)