check_phe_file_ok_for_qt: Check if a phenotype files holds a table that is valid for...

In richelbilderbeek/plinkr: Interface to PLINK

Check if a phenotype files holds a table that is valid for use in a quantitative trait analysis

Description

Check if a phenotype files holds a table that is valid for use in a quantitative trait analysis. Will stop if not

Usage

check_phe_file_ok_for_qt(phe_filename)

Arguments

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.

Details

For a phenotype table to be valid for use in a quantitative trait analysis, in each column, at least 1 value must differ from 0, 1, and 2. This is because PLINK will assume a case-control analysis when all values in a column are 0, 1 and 2.

Value

Nothing. Will stop if the phenotype table in the file is invalid for use in a quantitative trait analysis

Author(s)

Richèl J.C. Bilderbeek

See Also

Use check_phe_table_ok_for_qt to check if an in-memory phenotype table is valid for use in a quantitative trait analysis

Examples

phe_filename <- get_plinkr_filename("demo_assoc_qt.phe")
check_phe_file_ok_for_qt(phe_filename)

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