read_gemma_assoc: Read GEMMA statistics table

In OchoaLab/genbin: R wrappers for binaries in genetics

Read GEMMA statistics table

Description

Parses the output generated by GEMMA (genetic assocation test). Returned table has column names standardized for convenience. Validated with GEMMA version 0.98.1.

Usage

read_gemma_assoc(file, ext = "assoc.txt", verbose = TRUE)

Arguments

file	The file path to read, possibly missing the extension.
ext	The expected file extension. Set to NA to prevent adding any extension to file. The default "assoc.txt" extension matches what GEMMA generates.
verbose	If TRUE (default) function reports the path of the file being loaded (after autocompleting the extensions).

Value

The table as a tibble. Original names (as they appear in the header line of the file) are modified by these specific mappings to ensure that columns shared by BIM table have the same names as those returned by genio::read_bim(), the association p-value is "p", and the regression coefficient is "beta" ("orig" -> "new"):

• "rs" -> "id"

• "ps" -> "pos"

• "allele1" -> "alt"

• "allele0" -> "ref"

• "p_wald" -> "p"

See Also

gemma_lmm() wrapper for executing GEMMA and reading the results.

Examples

## Not run: 
data <- read_gemma_assoc( file )

## End(Not run)

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