gettract: gettract

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

gettract

Description

Generating tract from snp level ancestry call.

Usage

gettract(
  datadir,
  outputdir,
  indiv_name = "50",
  chr = "chrX",
  chrlength = "142711496",
  value = 35000,
  mode_n = 0.5,
  min_n = 20,
  exclude = 50000
)

Arguments

datadir	input snp level ancestry call file
outputdir	output tract file
indiv_name	The unique identifier for the individual, which could be numeric index (e.g. 1) or character sample name (e.g. "sample_1")
chr	the chromosome it is on
chrlength	the length of the chromosome
value	window size
mode_n	the minimum percentage for a call to be made using majority rule
min_n	the minimum number of SNPs within the window to make a call
exclude	how much of the start/end of each chromosome to ignore

Value

An output file including tract and majority rule

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