Pathway similarity and communities

Pathway similarity and communities

Usage

pathway_sim_comm(
  x,
  gs_list,
  method = c("overlap", "jaccard"),
  coeff = c(0.5, 0.1),
  all_gs = TRUE,
  comm_method = c("auto", "fastgreedy", "multilev"),
  set_sim_df = NULL
)

Arguments

x

named vector of pathway scores

gs_list

gene set list

method

'overlap' or 'jaccard'

coeff

threshold for the similarity score between two gene sets

all_gs

TRUE/FALSE

comm_method

one among 'auto', 'fastgreedy' and 'multilev'

set_sim_df

optional data frame with three columns 'set1', 'set2' and 'sim'

Value

list of two data frames containing pathway network and vertex similarity