MAF.cut {RAINBOWR}

Function to remove the minor alleles

Description

Function to remove the minor alleles

Usage

MAF.cut(
  x.0,
  map.0 = NULL,
  min.MAF = 0.05,
  max.HE = 0.999,
  max.MS = 0.05,
  return.MAF = FALSE
)

Arguments

x.0

A n \times m original marker genotype matrix.

map.0

Data frame with the marker names in the first column. The second and third columns contain the chromosome and map position.

min.MAF

Specifies the minimum minor allele frequency (MAF). If a marker has a MAF less than min.MAF, it is removed from the original marker genotype data.

max.HE

Specifies the maximum heterozygous rate (HE). If a marker has a HE more than max.HE, it is removed from the original marker genotype data.

max.MS

Specifies the maximum missing rate (MS). If a marker has a MS more than max.MS, it is removed from the original marker genotype data.

return.MAF

If TRUE, MAF will be returned.

Value

$x

The modified marker genotype data whose SNPs with MAF <= min.MAF were removed.

$map

The modified map information whose SNPs with MAF <= min.MAF were removed.

$before

Minor allele frequencies of the original marker genotype.

$after

Minor allele frequencies of the modified marker genotype.