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

Identify CpGs where methylation is associated with a continuous or categorical phenotype.

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`dat` |
A |

`pheno` |
The phenotype to be tested for association with methylation. |

`type` |
Is the phenotype '‘continuous’ or ‘categorical’? |

`qCutoff` |
DMPs with an FDR q-value greater than this will not be returned. |

`shrinkVar` |
Should variance shrinkage be used? See details. |

This function tests each genomic position for association between methylation and a phenotype. Continuous phenotypes are tested with linear regression, while an F-test is used for categorical phenotypes.

Variance shrinkage (`shrinkVar=TRUE`

) is recommended when sample
sizes are small (<10). The sample variances are squeezed
by computing empirical Bayes posterior means using the limma
package.

A table with one row per CpG.

Martin Aryee aryee@jhu.edu.

`squeezeVar`

and the limma package in general.

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