Quality Control
Quality Control (QC) and possible conversion to bed/bim/fam files using PLINK 1.9.
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 )
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 |
prefix.out |
Prefix (path without extension) of the bed/bim/fam dataset
to be created. Default is created by appending |
maf |
Minimum Minor Allele Frequency (MAF) for a SNP to be kept.
Default is |
geno |
Maximum proportion of missing values for a SNP to be kept.
Default is |
mind |
Maximum proportion of missing values for a sample to be kept.
Default is |
hwe |
Filters out all variants which have Hardy-Weinberg equilibrium
exact test p-value below the provided threshold. Default is |
autosome.only |
Whether to exclude all unplaced and non-autosomal
variants? Default is |
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 |
verbose |
Whether to show PLINK log? Default is |
The path of the newly created bedfile.
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. doi: 10.1186/s13742-015-0047-8.
## 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
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