pca: Do a principal component analysis

In richelbilderbeek/plinkr: Interface to PLINK

Do a principal component analysis

Description

Do a principal component analysis

Usage

pca(
  base_input_filename,
  base_output_filename,
  plink_options = create_plink_v1_9_options(),
  verbose = FALSE
)

Arguments

base_input_filename	the base of the filenames that are used as input for PLINK/PLINK2
base_output_filename	the base of the filenames that are used as output for PLINK/PLINK2
plink_options	options to run PLINK, as created by create_plink_options
verbose	the verbosity of a function. Set to TRUE for more output. Use check_verbose to detect if this argument is valid.

Value

a list of filenames that are created.

The list has elements:

• bed_filename: the .bed filename, as can be read by read_plink_bed_file

• bim_filename: the .bim filename, as can be read by read_plink_bim_file

• eigenval_filename: the .eigenval filename, as can be read by read_plink_eigenval_file

• eigenvec_filename: the .eigenvec filename, as can be read by read_plink_eigenvec_file

• fam_filename: the .fam filename, as can be read by read_plink_fam_file

• log_filename: the .log filename, as can be read by read_plink_log_file

Use check_pca_result_filenames

Note

this function is named after the PLINK/PLINK2 --pca parameter flag

Author(s)

Richèl J.C. Bilderbeek

richelbilderbeek/plinkr documentation built on March 25, 2024, 3:18 p.m.