filter.control: Set options for quality control filtering of data.

In CrypticIBDcheck: Identifying Cryptic Relatedness in Genetic Association Studies

Description

Set options for quality control filtering of data.

Usage

filter.control(filter=TRUE, snpcallrate=.9, MAF=.01, samplecallrate=.9, 
               HWEp=.001)

Arguments

filter	Should data filtering be done? Default is TRUE.
snpcallrate	The SNP call rate is the proportion of non-missing genotypes in the study per SNP. SNPs with call rate less than snpcallrate are removed. The default value is 0.90.
MAF	The minimum minor allele frequency (MAF) for SNPs. SNPs with MAF less than MAF are removed. The default value is 0.01.
samplecallrate	The proportion of SNPs for a sample that had genotype calls. Samples with call rate less than samplecallrate are removed. The default value is 0.90.
HWEp	Threshold for the p-value from a 2-sided test of HWE. SNPs with p-value less than HWEp are removed. The default value is 0.001.

Value

A list whose components are the function inputs.

Author(s)

Annick Joelle Nembot-Simo, Jinko Graham and Brad McNeney

See Also

IBDcheck

Examples

ff<-filter.control()
ff<-filter.control(MAF=0.05)

CrypticIBDcheck documentation built on May 2, 2019, 7:30 a.m.