formetascore {GenABEL}  R Documentation 
Function to run GWA analysis – using all functions available in GenABEL – and produce output oriented for future metaanalysis
formetascore(formula, data, stat = qtscore, transform = "no", build = "unknown", verbosity = 1, ...)
formula 
standard formula 
data 
object of gwaa.dataclass 
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 metaanalusis is aimed afterwards.
A transformation is applied to the formladefined residual, and the resulting trait is analysed with specified function. Results are arranged as dataframe.
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) Pvalue for the test (8) corrected Pvalue (we will use Genomic Control) (9) coding, with reference allele coming first (10) strand (11) frequency of the reference allele (12) Exact Pvalue for HWE test, etc. (depends on "verbosity" parameter.
Yurii Aulchenko
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,]