format_array_chr: format_array_chr

In mcanouil/rain: Reference-based Ancestry INference

format_array_chr

Description

format_array_chr

Usage

format_array_chr(
  cohort_name,
  input_vcfs,
  output_directory,
  ref1kg_vcfs,
  ref1kg_maf,
  quality_tag,
  quality_threshold,
  recode,
  n_cores,
  bin_path
)

Arguments

cohort_name	A character. A name to describe the studied population compared to 1,000 Genomes.
input_vcfs	A character. A path to one or several VCFs file.
output_directory	A character. The path where the data and figures is written.
ref1kg_vcfs	A character. A path to the reference VCFs files (i.e., 1,000 Genomes sequencing data).
ref1kg_maf	A numeric. MAF threshold for SNPs in 1,000 Genomes
quality_tag	A character. Name of the imputation quality tag for "array", e.g., "INFO" or "R2". Default is NULL.
quality_threshold	A numeric. The threshold to keep/discard SNPs based on their imputation quality.
recode	A character. Which VCF should be filtered and recode, either "all" or "input".
n_cores	An integer. The number of CPUs to use to estimate the ethnicity.
bin_path	A list(character). A list giving the binary path of vcftools, bcftools, bgzip, tabix and plink.

mcanouil/rain documentation built on Nov. 28, 2022, 10:40 a.m.