snprelate_qc: snprelate_qc

In ThomasChln/snpclust: SNP Feature Summarization for Unsupervised Clustering

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

ThomasChln/snpclust documentation built on June 11, 2020, 4:27 p.m.