Estimate the equivalence class of a directed acyclic graph (DAG) from observational data, using the PC_stable algorithm.

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`suffStat` |
A list of sufficient statistics, containing all necessary elements for the conditional independence decisions in the function indepTest. |

`indepTest` |
A function for testing conditional independence. It is internally called as indepTest(x,y,S,suffStat), and tests conditional independence of x and y given S. Here, x and y are variables, and S is a (possibly empty) vector of variables (all variables are denoted by their column numbers in the adjacency matrix). suffStat is a list, see the argument above. The return value of indepTest is the p-value of the test for conditional independence. |

`alpha` |
significance level (number in (0,1) for the individual conditional independence tests. |

`labels` |
(optional) character vector of variable (or "node") names. Typically preferred to specifying p. |

`p` |
(optional) number of variables (or nodes). May be specified if labels are not, in which case labels is set to 1:p. |

`fixedGaps` |
A logical matrix of dimension p*p. If entry [i,j] or [j,i] (or both) are TRUE, the edge i-j is removed before starting the algorithm. Therefore, this edge is guaranteed to be absent in the resulting graph. |

`fixedEdges` |
A logical matrix of dimension p*p. If entry [i,j] or [j,i] (or both) are TRUE, the edge i-j is never considered for removal. Therefore, this edge is guaranteed to be present in the resulting graph. |

`NAdelete` |
If indepTest returns NA and this option is TRUE, the corresponding edge is deleted. If this option is FALSE, the edge is not deleted. |

`m.max` |
Maximal size of the conditioning sets that are considered in the conditional independence tests. |

`u2pd` |
String specifying the method for dealing with conflicting information when trying to orient edges (see pcalg for details). |

`skel.method` |
Character string specifying method; the default, "stable" provides an order-independent skeleton. |

`conservative` |
Logical indicating if the conservative PC is used. In this case, only option u2pd = "relaxed" is supported. See pcalg for more information. |

`maj.rule` |
Logical indicating that the triples shall be checked for ambiguity using a majority rule idea, which is less strict than the conservative PC algorithm. For more information, see the pcalg package. |

`solve.confl` |
If TRUE, the orientation of the v-structures and the orientation rules work with lists for candidate sets and allow bi-directed edges to resolve conflicting edge orientations. In this case, only option u2pd = relaxed is supported. Note, that therefore the resulting object might not be a CPDAG because bi-directed edges might be present. See details for more information. |

`verbose` |
If TRUE, detailed output is provided. |

An object of class "pcAlgo" (see pcAlgo in the pcalg package) containing an estimate of the equivalence class of the underlying DAG.

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