ethseq.RM: Create Reference Model for Ancestry Analysis

In aromanel/EthSEQ: Ethnicity Annotation from Whole-Exome and Targeted Sequencing Data

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
)

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

Value

Logical value indicating the success of the analysis

aromanel/EthSEQ documentation built on March 22, 2023, 12:42 a.m.