estimate_ethnicity: estimate_ethnicity

Description Usage Arguments Value

View source: R/estimate_ethnicity.R

Description

estimate_ethnicity

Usage

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estimate_ethnicity(cohort_name, input_vcfs, input_type, output_directory,
  ref1kg_vcfs, ref1kg_population, ref1kg_maf = 0.05,
  splitted_by_chr = TRUE, quality_tag = NULL,
  quality_threshold = 0.9, recode = "all", vcf_half_call = "missing",
  n_cores = 6, bin_path = list(vcftools = "/usr/bin/vcftools", bcftools
  = "/usr/bin/bcftools", bgzip = "/usr/bin/bgzip", tabix =
  "/usr/bin/tabix", plink1.9 = "/usr/bin/plink1.9"))

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.

input_type

A character. Either "array" or "sequencing".

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_population

A character. A file which describe samples and their ethnicity.

ref1kg_maf

A numeric. MAF threshold for SNPs in 1,000 Genomes

splitted_by_chr

A logical. Is the VCFs files splitted by chromosome?

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".

vcf_half_call

A character. The mode to handle half-call. + 'haploid'/'h': Treat half-calls as haploid/homozygous (the PLINK 1 file format does not distinguish between the two). This maximizes similarity between the VCF and BCF2 parsers. + 'missing'/'m': Treat half-calls as missing (default). + 'reference'/'r': Treat the missing part as reference.

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.

Value

A data.frame.


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