index_samples: A function to align genotype and phenotype data

In plmmr: Penalized Linear Mixed Models for Correlated Data

A function to align genotype and phenotype data

Description

A function to align genotype and phenotype data

Usage

index_samples(
  obj,
  rds_dir,
  indiv_id,
  add_outcome,
  outcome_id,
  outcome_col,
  na_outcome_vals,
  outfile,
  quiet
)

Arguments

obj	An object created by process_plink()
rds_dir	The path to the directory in which you want to create the new '.rds' and '.bk' files.
indiv_id	A character string indicating the ID column name in the 'fam' element of the genotype data list. Defaults to 'sample.ID', equivalent to 'IID' in PLINK. The other option is 'family.ID', equivalent to 'FID' in PLINK.
add_outcome	A data frame with at least two columns: and ID column and a phenotype column
outcome_id	A string specifying the name of the ID column in pheno
outcome_col	A string specifying the name of the phenotype column in pheno. This column will be used as the default y argument to 'plmm()'.
na_outcome_vals	A vector of numeric values used to code NA values in the outcome. Defaults to c(-9, NA_integer) (the -9 matches PLINK conventions).
outfile	A string with the name of the filepath for the log file
quiet	Logical: should messages be printed to the console? Defaults to FALSE (which leaves the print messages on...

Value

a list with two items:

• a data.table with rows corresponding to the samples for which both genotype and phenotype are available.

• a numeric vector with indices indicating which samples were 'complete' (i.e., which samples from add_outcome had corresponding data in the PLINK files)

plmmr documentation built on April 4, 2025, 12:19 a.m.