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

rLCLAE

R Documentation

rLCLAE

Description

The summarized pipeline for rLCLAE

Usage

rLCLAE(
  input,
  tmp,
  output,
  chrlist,
  refpop1_dip,
  refpop2_dip,
  test_ind = "all",
  inputtype = "dip",
  freqtype = "dip",
  window = 50000,
  mode_min = 0.3,
  n_min = 10,
  delta = 0.1,
  exclude = 1000,
  inputdir_hap = "missing",
  refpop1_hap = "missing",
  refpop2_hap = "missing",
  mergetype = "union",
  zero_value = 10^(-7)
)

Arguments

`input`	vcf input
`tmp`	intermediate file storage
`output`	final output (not yet used)
`chrlist`	a data frame for chr name & length, from fai
`refpop1_dip`	numeric vector for index of ref ind for pop1, need expand
`refpop2_dip`	numeric vector for index of ref ind for pop2, need expand
`test_ind`	numeric vector for index of test individual, default all
`inputtype`	hap or dip
`freqtype`	hap, dip or merge
`window`	window size
`mode_min`	mode min
`n_min`	n min in window
`delta`	freq diff lower cutoff
`exclude`	exclude length
`inputdir_hap`	missing, do not touch, not finished for ancfreq
`refpop1_hap`	missing, do not touch, not finished for ancfreq
`refpop2_hap`	missing, do not touch, not finished for ancfreq
`mergetype`	union, do not touch, not finished for ancfreq
`zero_value`	a small zero value added to the zeros, if zero then throw out sites with any zero