compute_pca: Compute the genomic components (and some figures) for...

View source: R/compute_pca.R

compute_pcaR Documentation

Compute the genomic components (and some figures) for ethnicity based on VCF files.

Description

Compute the genomic components (and some figures) for ethnicity based on VCF files.

Usage

compute_pca(
  cohort_name,
  input_plink,
  output_directory,
  ref1kg_population,
  n_comp = 10
)

Arguments

cohort_name

A character. A name to describe the studied population compared to 1,000 Genomes.

input_plink

A character. The path to plink format files (i.e., .bed, .bim and .fam files).

output_directory

A character. The path where the data and figures is written.

ref1kg_population

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

n_comp

A numeric. The number of principal components to be computed.

Value

A data.frame.


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