snprelate_qc {snplinkage}

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