Description Usage Arguments Value

View source: R/TreeBasedMethods.R

Applies the Simple PPT algorithm onto the expression data.

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`exprData` |
Expression data – Num_Genes x Num_Samples |

`numCores` |
Number of cores to use during this analysis |

`permExprData` |
a list of permutated expression datasets, to use for significance estimation of the tree [default:NULL] |

`nNodes_` |
Number of nodes to find. Default is sqrt(N) |

`sigma` |
regularization parameter for soft-assignment of data points to nodes, used as the variance of a guassian kernel. If 0, this is estimated automatically |

`gamma` |
graph-level regularization parameter, controlling the tradeoff between the noise-levels in the data and the graph smoothness. If 0, this is estimated automatically. |

Information on the fitten tree

C: spatial positions of the tree nodes in NUM_PROTEINS dimensional space

W: Unweighted (binary) adjacency matrix of the fitten tree

distMat: distance matrix between each tree node to each datapoint

mse: the Mean-Squared-Error of the fitten tree

zscore: a significance score for the fitted tree

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