formetascore {GenABEL} | R Documentation |
Function to run GWA analysis – using all functions available in GenABEL – and produce output oriented for future meta-analysis
formetascore(formula, data, stat = qtscore, transform = ztransform, 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 . It can also be equal to
"no" if no transformation is required.
|
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
data(ge03d2c) x <- formetascore(bmi ~ sex+age,ge03d2c) x[1:10,] x <- formetascore(bmi ~ sex+age,ge03d2c,trans=rntransform) x[1:10,] x <- formetascore(bmi ~ sex+age,ge03d2c,trans=rntransform,verbosity=2) x[1:10,]