sort.dnapath_list | R Documentation |

Sort function for 'dnapath_list' object.

## S3 method for class 'dnapath_list' sort(x, decreasing = TRUE, by = "dc_score", ...)

`x` |
A 'dnapath_list' object from |

`decreasing` |
Logical. If TRUE (the default), results are sorted in decreasing order. |

`by` |
The variable to sort the results by. Must be one of: "mean_expr", the mean expression of each pathway across both groups; "mean_expr1" or "mean_expr2", the mean expression of each pathway in group 1 or 2, respectively; "dc_score", the differential connectivity score of the pathway; "p_value", the p-value of the dc score; "n_genes", the number of genes in each pathway; "pathway", the pathway names; or "n_dc" the number of significantly differentially conncted genes in each pathway. |

`...` |
Additional arguments are ignored. |

The differential network analysis results ordered by DC pathway score.

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) # Filter out pathways that have p-values above 0.2. results_sig <- filter_pathways(results, 0.2) sort(results_sig, by = "dc_score") # Sort by the pathway DC score. sort(results_sig, by = "n_genes") # Sort by the pathway size. sort(results_sig, by = "mean_expr") # Sort by the mean expression.

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