anccall: anccall

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

anccall

Description

anccall

Usage

anccall(
  inputdir,
  outputdir,
  chrom_name,
  indiv_name,
  mode_min = 0.5,
  n_min = 20,
  delta = 0.2,
  window_size = 50000,
  round1 = 1,
  round2 = 1,
  round3 = 2,
  auto_optimize = F,
  ploidy = "dip",
  chrlength = 142711496,
  zero_value = 10^(-7)
)

Arguments

inputdir	The file to the ancestral likelihood file
outputdir	The file to store the ancestry call
chrom_name	The name of the chromosome
indiv_name	The unique identifier for the individual, which could be numeric index (e.g. 1) or character sample name (e.g. "sample_1")
mode_min	The minimum percentage for the mode to make a call, default set to 0.5
n_min	the minimum number of SNPs within the window to make a call, default set to zero
delta	The cutoff for ancestral allele frequency difference
window_size	The size of the sliding window
round3	The scaler for window_size for third round
ploidy	"hap" or "dip", default set to "dip"
chrlength	chromosome length, default set to baboon X: 142711496
zero_value	The small value added to avoid zeroes, default to 10^-7

Value

nothing

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