EthSEQ (version 3.0.2)

ethseq.RM: Create Reference Model for Ancestry Analysis

Description

This function creates a GDS reference model that can be used to performe EthSEQ ancestry analysis

Usage

ethseq.RM(
  vcf.fn,
  annotations,
  out.dir = "./",
  model.name = "Reference.Model",
  bed.fn = NA,
  verbose = TRUE,
  call.rate = 1,
  cores = 1
)

Value

Logical value indicating the success of the analysis

Arguments

vcf.fn

vector of paths to genotype files in VCF format

annotations

data.frame with mapping of all samples names, ancestries and gender

out.dir

Path to output folder

model.name

Name of the output model

bed.fn

path to BED file with regions of interest

verbose

Print detailed information

call.rate

SNPs call rate cutoff for inclusion in the final reference model

cores

How many parallel cores to use in the reference model generation