formetascore: function to run GWA analysis oriented for future...
In GenABEL: genome-wide SNP association analysis

Description Usage Arguments Details Value Author(s) See Also Examples

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

1 2	formetascore(formula, data, stat = qtscore, transform = "no", build = "unknown", verbosity = 1, ...)

`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

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.

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.

Yurii Aulchenko

ztransform,qtscore

	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,]