filter.control {CrypticIBDcheck}R Documentation

Set options for quality control filtering of data.

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)

[Package CrypticIBDcheck version 0.3-3 Index]