name_and_count_bigsnp: A helper function to label and summarize the contents of a...

In plmmr: Penalized Linear Mixed Models for Correlated Data

A helper function to label and summarize the contents of a bigSNP

Description

A helper function to label and summarize the contents of a bigSNP

Usage

name_and_count_bigsnp(obj, id_var, quiet, outfile)

Arguments

obj	a bigSNP object, possibly subset by add_external_phenotype()
id_var	String specifying which column of the PLINK .fam file has the unique sample identifiers. Options are "IID" (default) and "FID".
quiet	Logical: should messages be printed to the console? Defaults to TRUE
outfile	The string with the name of the .log file

Value

a list with components:

• counts: column-wise summary of the minor allele counts in 'genotypes'

• obj: a modified bigSNP list with additional components

• X: the obj$genotypes as its own FBM

• pos: the obj$map$physical.pos vector

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