ancfreq: ancfreq

In lycium0605/rLCLAE: Implement Low Coverage Local Ancestry Estimation in R

ancfreq

Description

A function to calculate ancestral allele frequency based on two reference populations.

Usage

ancfreq(
  outputdir,
  inputdir_dip = "missing",
  pop1_dip = "missing",
  pop2_dip = "missing",
  inputdir_hap = "missing",
  pop1_hap = "missing",
  pop2_hap = "missing",
  mergetype = "union"
)

Arguments

outputdir	The dir to the output file. A postfix ('_dip','_hap','_merge') will be added.
inputdir_dip	The dir to a file containing diploid genotype likelihood data.
pop1_dip	A numeric vector specifying the index of reference population 1 for diploid data.
pop2_dip	A numeric vector specifying the index of reference population 2 for diploid data.
inputdir_hap	The dir to a file containing haploid genotype likelihood data.
pop1_hap	A numeric vector specifying the index of reference population 1 for haploid data.
pop2_hap	A numeric vector specifying the index of reference population 2 for haploid data.
mergetype	A parameter for merging type ("intersect","union","full_dip","full_hap")

Value

The output for ancfreq consists of a single line for each SNP. The first field shows the base position; the second to third fields show the estimated allele frequency for reference population 1 and 2; the third field shows the estimated difference in allele frequency in the two reference populations, the fourth to fifth fields show available individuals in reference population one and two.

lycium0605/rLCLAE documentation built on Aug. 28, 2024, 11:35 p.m.