R: function to run GWA analysis oriented for future...

formetascore {GenABEL} | R Documentation

## function to run GWA analysis oriented for future meta-analysis

### Description

Function to run GWA analysis – using all functions available in GenABEL – and produce output oriented for future meta-analysis

### Usage

    formetascore(formula, data, stat = qtscore, transform = "no",
    		build = "unknown", verbosity = 1, ...)

### Arguments

`formula` | standard formula
`data` | object of `gwaa.data-class`
`stat` | which GWA analysis function to apply. Could be `mlreg`, `qtscore`, `mmscore`, `grammar`, `egscore`, etc.
`transform` | Which trait transform to apply, could be `ztransform` or `rntransform`. Default value is "no" – no transformation.
`build` | if you need that in output, specify genomic build here (e.g. "35")
`verbosity` | how much output is produced? Possible values are 0, 1, and 2
`...` | further arguments, passed to the ”stat” GWA analysis function

### Details

This function should be applied to analysis of quantitative traits, if meta-analusis is aimed afterwards.

A transformation is applied to the formla-defined residual, and the resulting trait is analysed with specified function. Results are arranged as data-frame.

### Value

Data frame, containing GWA summary. The fields include: (1) SNP name (2) chromosome (3) position (4) number of people with available data (5) effect of the allele (6) standard error of the effect (7) P-value for the test (8) corrected P-value (we will use Genomic Control) (9) coding, with reference allele coming first (10) strand (11) frequency of the reference allele (12) Exact P-value for HWE test, etc. (depends on "verbosity" parameter.

### Author(s)

Yurii Aulchenko

### See Also

`ztransform`,`qtscore`

### Examples

    	require(GenABEL.data)
    	data(ge03d2c)
    	x <- formetascore(bmi ~ sex+age,ge03d2c)
    	x[1:10,]
    	x <- formetascore(bmi ~ sex+age,ge03d2c,trans=ztransform)
    	x[1:10,]
    	x <- formetascore(bmi ~ sex+age,ge03d2c,trans=rntransform,verbosity=2)
    	x[1:10,]

[Package GenABEL version 1.8-0 Index]