snprelate_qc: snprelate_qc

In snplinkage: Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations

snprelate_qc

Description

Quality control using SNPRelate functions.

Usage

snprelate_qc(
  gdata,
  samples_nas = 0.03,
  ibs = 0.99,
  keep_ids = NULL,
  snps_nas = 0.01,
  maf = 0.05,
  tagsnp = 0.8,
  n_cores = 1
)

Arguments

gdata	Genotype data object
samples_nas	NA threshold for samples, default 3 pct
ibs	Samples identity by state threshold, default 99 pct
keep_ids	Samples ids to keep even if IBS is higher than threshold. Used for monozygotic twins.
snps_nas	NA threshold for SNPs, default 1 pct
maf	Minor allele frequency threshold, default 5 pct
tagsnp	TagSNP r2 correlation threshold, default 0.8
n_cores	Number of cores

Value

List of gdata, Genotype data object, and df_qc, QC info data frame

Examples

library(snplinkage)
gds_path <- save_hgdp_as_gds()
gdata <- load_gds_as_genotype_data(gds_path)
qc <- snprelate_qc(gdata, tagsnp = .99)

snplinkage documentation built on Sept. 11, 2024, 6:02 p.m.