snp_plinkQC: Quality Control

In bigsnpr: Analysis of Massive SNP Arrays

Quality Control

Description

Quality Control (QC) and possible conversion to bed/bim/fam files using PLINK 1.9.

Usage

snp_plinkQC(
  plink.path,
  prefix.in,
  file.type = "--bfile",
  prefix.out = paste0(prefix.in, "_QC"),
  maf = 0.01,
  geno = 0.1,
  mind = 0.1,
  hwe = 1e-50,
  autosome.only = FALSE,
  extra.options = "",
  verbose = TRUE
)

Arguments

plink.path	Path to the executable of PLINK 1.9.
prefix.in	Prefix (path without extension) of the dataset to be QCed.
file.type	Type of the dataset to be QCed. Default is "--bfile" and corresponds to bed/bim/fam files. You can also use "--file" for ped/map files, "--vcf" for a VCF file, or "--gzvcf" for a gzipped VCF. More information can be found at https://www.cog-genomics.org/plink/1.9/input.
prefix.out	Prefix (path without extension) of the bed/bim/fam dataset to be created. Default is created by appending "_QC" to prefix.in.
maf	Minimum Minor Allele Frequency (MAF) for a SNP to be kept. Default is 0.01.
geno	Maximum proportion of missing values for a SNP to be kept. Default is 0.1.
mind	Maximum proportion of missing values for a sample to be kept. Default is 0.1.
hwe	Filters out all variants which have Hardy-Weinberg equilibrium exact test p-value below the provided threshold. Default is 1e-50.
autosome.only	Whether to exclude all unplaced and non-autosomal variants? Default is FALSE.
extra.options	Other options to be passed to PLINK as a string. More options can be found at https://www.cog-genomics.org/plink2/filter. If using PLINK 2.0, you could e.g. use "--king-cutoff 0.0884" to remove some related samples at the same time of quality controls.
verbose	Whether to show PLINK log? Default is TRUE.

Value

The path of the newly created bedfile.

References

Chang, Christopher C, Carson C Chow, Laurent CAM Tellier, Shashaank Vattikuti, Shaun M Purcell, and James J Lee. 2015. Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience 4 (1): 7. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1186/s13742-015-0047-8")}.

See Also

download_plink snp_plinkIBDQC

Examples

## Not run: 

bedfile <- system.file("extdata", "example.bed", package = "bigsnpr")
prefix  <- sub_bed(bedfile)
plink <- download_plink()
test <- snp_plinkQC(plink.path = plink,
                    prefix.in = prefix,
                    prefix.out = tempfile(),
                    file.type = "--bfile",  # the default (for ".bed")
                    maf = 0.05,
                    geno = 0.05,
                    mind = 0.05,
                    hwe = 1e-10,
                    autosome.only = TRUE)
test

## End(Not run)

bigsnpr documentation built on Sept. 30, 2024, 9:18 a.m.