Description Usage Arguments Examples

Parameters for mapping mixture components to distinct copy number states

1 2 3 |

`threshold` |
numeric value in [0, 0.5]. For a given observation (sample), mixture component probabilities > threshold and less than 1-threshold are combined. |

`proportion.subjects` |
numeric value in [0, 1]. Two components are combined if the fraction of subjects with component probabilities in the range [threshold, 1-threshold] exceeds this value. |

`outlier.variance.ratio` |
if the ratio of the component variance to the median variance of the other component exceeds the value of this argument, the component is considered to correspond to outliers. |

`max.homozygous` |
length-2 numeric vector of cutoffs used for establishing a homozygous deletion component. The first element is the cutoff for the mean log R ratios when there are 2 or more states. The second element is the cutoff for the mean log R ratio when there are 3 or more states. |

`min.foldchange` |
a length-one numeric vector. When there are 3 or more
states, we compute the ratio of the distance between the means of the
sorted components 1 and 2 (the 2 components with lowest means) and the
distance between the means of components 2 and 3. If the ratio (i) exceeds
the value specified by this parameter, (ii) there are 3 or more states, and
(iii) the first component has a mean less than |

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