haplotype wide association study (hwas)

This package contains tools for running an HWAS interactively (e.g. interactive R console or Jupyter notebook) or semi- automatically by a programmatic pipeline. The data are read from the vcf, vcf.gz, or bcf file format with htslib [1, 2] and the statistics by code from Karl Broman's QTL2 [3, 4].

Contents

HWAS tools Pipeline Instructions Compiling and Installation Testing C++ Code Features Outstanding AI Disclosure Copyright References

HWAS tools

Please checkout the package vignettes for examples using the hwas package tools.

Compiling and Installation

HTSLIB

This package depends on the systems htslib. The location of htslib header and library files may be determined by pkg-config or setting environment variables:

export HTSLIB_CPATH=<PATH_TO_HEADER_FILES>
export HTSLIB_LIB_PATH=<PATH_TO_LIBRARY_FILE>

Note, that if both are configured the variables defined in pkg-config are used.

R LIBRARY TREE

When building the package be mindful that vignettes are also built from source. When R builds the package vignette it doesn't read a users Rprofile file. Consequently, the hwas package dependency needs to be installed either in the default R library path or that the environment variable R_LIBS contains the path to the relevant library directory.

Testing C++ code

The hwas package uses C/C++ libraries and is connected to R by Rcpp. The result a combination of Rcpp independent and dependent C++ code. We've created GoogleTest based unit tests for the Rcpp independent C++ code. These tests can be run using the Makefile in the root of the source package. Simply,

make tests

and the code will be built and tested.

Features outstanding

• initialization functionality
• heritability script
• lod script
• blup script
• test against qtl2

AI Disclaimer

The AI, Claude 4.7- Opus by Anthropic was used to review code, architectural recommendations / discussions, and in very few cases contributed code. Any code contributed by Claude will be made known in the code comments or in the git logs.

Copyright Notice

Portions from the linear mixed model fitting code are:

• Copyright (C) 2020 Karl Browman
• Copyright (C) 1995, 1996 Robert Gentleman and Ross Ihaka,
• Copyright (C) 1998-2014 The R Core Team

References

[1] HTSLIB citation [2] https://github.com/samtools/htslib [3] QTL2 citation [4] https://github.com/rqtl/qtl2