format_array_chr: format_array_chr

Description Usage Arguments

View source: R/estimate_ethnicity.R

Description

format_array_chr

Usage

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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 plink1.9.


mcanouil/CARoT documentation built on Oct. 17, 2019, 4:36 p.m.