freq_from_bfile_within_phe_file: Let 'PLINK'/'PLINK2' calculate the allele frequencies per...

In richelbilderbeek/plinkr: Interface to PLINK

Let PLINK/PLINK2 calculate the allele frequencies per phenotype.

Description

Let PLINK/PLINK2 calculate the allele frequencies per phenotype, from PLINK1 binary filenames

Usage

freq_from_bfile_within_phe_file(
  bfile,
  phe_filename,
  out,
  plink_options = create_plink_options(),
  verbose = FALSE
)

Arguments

bfile	the base filename of the binary files (i.e. a .bed, .bim and .fam file). This parameter is named after the PLINK --bfile flag
phe_filename	name of a phenotype (.phe) file, as checked by check_phe_filename. Use read_plink_phe_file to read a raw phenotype file.
out	the base filename of the output files. This parameter is named after the PLINK --out flag
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 with the following elements:

• frq_table table with ?

• log the log text

Note

This function is named after the --freq flag used by PLINK

Author(s)

Richèl J.C. Bilderbeek

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