Description Usage Arguments Details Value Author(s) References See Also Examples
The function performs genome-wide association scan based on predictive ability evaluated via cross validation.
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formula |
Formula describing fixed effects to be used in analysis, e.g. y ~ a + b means that outcome (y) depends on two covariates, a and b. If no covariates used in analysis, please skip the right-hand side of the equation. |
data |
An (optional) object of
|
nfolds |
Number of folds to be established during the cross validation. |
seed |
A positive integer to set seed for
randomization so that the results can be exactly
repeated. If |
verbose |
A logic value to set whether more screen displayed output is shown during the procedure. |
... |
Other parameters to be passed. |
The predictive ability is assessed by an $R^2$ value, which is the squared correlation coefficient between the predicted phenotypes and their true values for each variant. In each fold of the cross validation, such an $R^2$ value is calculated, then the final estimate of $R^2$ is given by the mean of all such values from the cross validation.
A list containing R2.est
, R2.raw
and
R.raw
which provide the estimated $R^2$ for each
variant, the orginal $R^2$ values from cross validation,
and the corresponding $R$ values.
Xia Shen
Shen X (2013). The missing heritability revealed in Arabidopsis thaliana. Submitted.
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