bolt_lmm: Run BOLT-LMM '–lmm' and returns table of association...

In OchoaLab/genbin: R wrappers for binaries in genetics

Run BOLT-LMM --lmm and returns table of association statistics.

Description

A wrapper for running BOLT-LMM's genetic association test followed by reading of the results by read_bolt_lmm(). In addition to the arguments listed below, the executable is run with --phenoUseFam (so the phenotype tested can only be the one present in the input FAM file), --LDscoresUseChip, --lmmForceNonInf (so columns are never missing), and ⁠--maxMissingPerSnp 1 --maxMissingPerIndiv 1⁠ (so full data is used and loci are never missing from table).

Usage

bolt_lmm(name, name_out = name, bolt_bin = "bolt", threads = 0, verbose = TRUE)

Arguments

name	The shared name of the input plink BED/BIM/FAM files without extensions (the argument to --bfile).
name_out	The base name of the output statistics file (the argument to --statsFile; default same as input name), which gets extension ".bolt.lmm" added automatically.
bolt_bin	The path to the binary executable. Default assumes bolt is in the PATH.
threads	The number of threads to use (the argument to --numThreads). The values 0 (default), NA, or NULL use all threads available (the output of parallel::detectCores()).
verbose	If TRUE (default), prints the command line before it is executed, followed by the the path of the output file being read (after autocompleting the extensions).

Value

The table of genetic association statistics, as a tibble, read with read_bolt_lmm() (see that for more info).

See Also

read_bolt_lmm() for parsing the output of BOLT-LMM.

delete_files_bolt() for deleting the output of BOLT-LMM.

system3(), used (with ret = FALSE) for executing BOLT-LMM and error handling.

Examples

## Not run: 
data <- bolt_lmm( name, name_out )

## End(Not run)

OchoaLab/genbin documentation built on Nov. 14, 2024, 7:33 p.m.