summarize_edges | R Documentation |

Summarize differential connections for a pathway

summarize_edges(x, alpha = 0.1, monotonized = FALSE, require_dc_genes = FALSE)

`x` |
A 'dnapath' object from |

`alpha` |
Threshold for p-values of edge DC scores. Defaults to 0.1 or the minimum possible threshold for the number of permutations performed, whichever is greater. |

`monotonized` |
If TRUE, monotonized p-values are used. |

`require_dc_genes` |
If TRUE, the gene-level differential connectivity p-value of the two genes for a given edge are also considered when deciding whether an edge is differentially connected. If neither gene is significantly differentially connected, then the edge between them will not be either. |

A tibble summarizing the differential connections in the pathway.

`summarize_pathways`

, `summarize_genes`

data(meso) data(p53_pathways) set.seed(0) results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways, group_labels = meso$groups, n_perm = 10) summarize_edges(results[[1]])

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