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

ancgen

R Documentation

ancgen

Description

A general wrapped-up function for steps after ancestral frequency estimation.

Usage

ancgen(
  genodir,
  ancfreqdir,
  outputdir,
  type = "dip",
  test = "all",
  delta,
  window,
  chrlength,
  mode_n = 0.5,
  min_n = 20,
  exclude = 50000
)

Arguments

`genodir`	The directory to genolik file.
`ancfreqdir`	The directory to ancestral frequency file.
`outputdir`	The folder to save output files.
`type`	'dip' for diploid data (default) and 'hap' for haploid data.
`test`	The individuals to be tested. 'all' for all individuals (default), or a numeric vector containing the individual number to be estimated
`delta`	The cutoff for ancestral allele frequency difference
`window`	The size of the sliding window for round 1 and 2, and half of the sliding window for round 3.
`chrlength`	A list of the length to the chromosome.
`mode_n`	The minimum percentage for the mode to make a call, default set to 0.5.
`min_n`	The minimum number of SNPs within the window to make a call, default set to zero.
`exclude`	The length of the start/end of each chromosome to ignore.