permutePhe

phe_file

character. Path to permuted phenotype file.

out_file

logical. When set to TRUE, existing file is overwritten.

force

logical. Whether to validate the phenotype file first.

valid


All columns except FID and IID are permuted.


Implements a generalized version of the CDH test (<DOI:10.1371/journal.pone.0028145> and <DOI:10.1186/s12859-016-1006-9>)
for detecting compound heterozygosity on a
genome-wide level, due to usage of generalized linear models it allows flexible
analysis of binary and continuous traits with covariates.

permutePhe: Permute a phenotype file

Description

Usage

Arguments