R: Sort function for 'dnapath_list' object.

sort.dnapath_list {dnapath} | R Documentation

## Sort function for 'dnapath_list' object.

### Description

Sort function for 'dnapath_list' object.

### Usage

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

### Arguments

`x` | A 'dnapath_list' object from `dnapath`.
`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.

### Value

The differential network analysis results ordered by DC pathway score.

### Examples

    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.

[Package dnapath version 0.7.4 Index]