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

A function which estimates the variogram of the z-scores in the given data frame.

1 | ```
makeVariogram(test.out, make.variogram, sample.clusters, max.dist)
``` |

`test.out` |
A |

`make.variogram` |
A |

`sample.clusters` |
Can speed up variogram estimation
significantly. Default is |

`max.dist` |
Can speed up variogram estimation significantly. The variogram is estimated for distances until this threshold. Default is 500 base pairs, since the variogram usually does not change for distances larger than 100 base pairs, because methylation of CpG sites further away are not correlated anymore. Especially useful if there are large clusters. |

For each CpG site the z-score is determined by `qnorm`

(1 -
P value). The variogram of the z-scores of locations *k*
and *l* within one cluster is estimated robustly by

*
2 \hat{γ}(h) = [median{(Z_{k}-Z_{l})^2: (s_{k}, s_{l}) \in
N(h)}] / .455
*

.

A list:

`variogram ` |
A |

`pValsList ` |
A |

Katja Hebestreit

Yoav Benjamini and Ruth Heller (2007): False Discovery Rates for Spatial Signals. American Statistical Association, 102 (480): 1272-81.

1 2 3 4 5 | ```
data(betaResults)
vario <- makeVariogram(betaResults)
plot(vario$variogram$v)
``` |

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