estimate_ethnicity: Format VCF files and compute the genomic components (and some...
In mcanouil/rain: Reference-based Ancestry INference

View source: R/estimate_ethnicity.R

estimate_ethnicity

R Documentation

Format VCF files and compute the genomic components (and some figures) for ethnicity.

Description

Format VCF files and compute the genomic components (and some figures) for ethnicity.

Usage

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_comp = 10,
  n_cores = 6,
  bin_path = list(vcftools = "/usr/bin/vcftools", bcftools = "/usr/bin/bcftools", bgzip
    = "/usr/bin/bgzip", tabix = "/usr/bin/tabix", plink = "/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_comp`	A `numeric`. The number of principal components to be computed.
`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`.