sort.dnapath_list: Sort function for 'dnapath_list' object.

In dnapath: Differential Network Analysis using Gene Pathways

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.

dnapath documentation built on April 3, 2025, 8:32 p.m.