assoc_adjust_from_bfile: Let 'PLINK'/'PLINK2' do a binary-trait/case-control...

In richelbilderbeek/plinkr: Interface to PLINK

Let PLINK/PLINK2 do a binary-trait/case-control association

Description

Let PLINK/PLINK2 do a binary-trait/case-control association from PLINK1 binary filenames

Usage

assoc_adjust_from_bfile(
  bfile,
  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
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 columns:

• assoc_table: a tibble with associations found by PLINK. See read_plink_assoc_file for an explanation of the column names.

• assoc_adjusted_table: a tibble with adjusted associations found by PLINK. See read_plink_assoc_adjusted_file for an explanation of the column names.

• log: the log file as text as created by PLINK

Note

This function is named after the --assoc --adjust flags used by PLINK

Author(s)

Richèl J.C. Bilderbeek

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