Identify Functional Modules Across Different Databases

Source: R/11-merge_modules.R

This function identify functional modules from various databases, such as GO, KEGG, and Reactome. It calculates the similarity matrix between all the pathways and clusters them into functional modules.

merge_modules(
  object,
  sim.cutoff = 0.5,
  measure_method = c("jaccard"),
  path = "result",
  save_to_local = FALSE
)

Arguments

object

An S4 object, expected to be processed by merge_pathways().

sim.cutoff

A numerical value for similarity cutoff, default is 0.5.

measure_method

A character vector indicating the method for measuring similarity, default is "jaccard".

path

A character string for the directory where to save results, default is "result".

save_to_local

Logical, if TRUE the results will be saved to local disk.

Note

Please ensure that object has been processed by merge_pathways() before using this function.

Author

Xiaotao Shen shenxt1990@outlook.com

Examples

if (FALSE) {
merge_modules(variable_info = my_var_info, object = my_object)
}