pathfindR (version 1.2.3)

calculate_pwd: Calculate Pairwise Distances Between Given Pathways

Description

Calculate Pairwise Distances Between Given Pathways

Usage

calculate_pwd(pathway_ids, pathway_names, agg_method = "average",
  plot_heatmap = FALSE, use_names = FALSE, custom_genes = NULL)

Arguments

pathway_ids

Vector of IDs of pathways to be used for calculation of pairwise distances.

pathway_names

Vector of names of pathways to be used for calculation of pairwise distances.

agg_method

the agglomeration method to be used if plotting heatmap (see next argument, default: average).

plot_heatmap

boolean value indicating whether or not to plot the heat map of pathway clustering (default: FALSE).

use_names

boolean value indicating whether to use gene set names instead of gene set ids (default: FALSE)

custom_genes

a list containing the genes involved in each custom pathway. Each element is a vector of gene symbols located in the given pathway. Names correspond to the ID of the pathway. Must be provided if pathways were obtained using custom gene sets.

Value

Pairwise distance matrix. Optionally plots a heatmap of pathway clustering.

Details

See "Chen, Y. A. et al. Integrated pathway clusters with coherent biological themes for target prioritisation. PLoS One 9, e99030, doi:10.1371/journal.pone.0099030 (2014)." for details on the method of pathway clustering.

See Also

hclust for hierarchical clustering, heatmap for drawing a heatmap.

Examples

# NOT RUN {
calculate_pwd(RA_output$ID)
# }