read_gcta_mlma: Read GCTA MLMA statistics table

In OchoaLab/genbin: R wrappers for binaries in genetics

Read GCTA MLMA statistics table

Description

Parses the output generated by GCTA with option --mlma (genetic assocation test). Returned table has column names standardized for convenience. Validated with GCTA version 1.93.2 beta.

Usage

read_gcta_mlma(file, ext = "mlma", 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 extension "mlma" agrees with the output of gcta_mlma().
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 lowercasing all, followed 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"):

• "snp" -> "id"

• "bp" -> "pos"

• "a1" -> "alt"

• "a2" -> "ref"

• "b" -> "beta"

See Also

gcta_mlma() wrapper for executing GCTA MLMA and reading the results.

Examples

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

## End(Not run)

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