read_emmax_ps: Read EMMAX statistics table

In OchoaLab/genbin: R wrappers for binaries in genetics

Read EMMAX statistics table

Description

Parses the output generated by EMMAX (genetic assocation test). Returned table has standard column names.

Usage

read_emmax_ps(file, maf = NULL, ext = "ps", verbose = TRUE)

Arguments

file	The file path to read, possibly missing the extension.
maf	Optional vector of allele frequencies (misnamed, these cannot be minor allele frequencies or nothing gets corrected), used to correct signs of regression coefficients (EMMAX reports them in terms of the major allele, not the original allele). If missing, no corrections are applied.
ext	The expected file extension. Set to NA to prevent adding any extension to file. The default "ps" extension matches what EMMAX generates.
verbose	If TRUE (default) function reports the path of the file being loaded (after autocompleting the extensions).

Value

The table as a tibble. The original does not have a header line. Output has 3 columns named: "id", "beta", "p".

See Also

emmax_lmm() wrapper for executing EMMAX and reading the results.

Examples

## Not run: 
data <- read_emmax_ps( file, maf )

## End(Not run)

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