CONDOR (COmplex Network Description Of Regulators) implements methods for clustering biapartite networks and estimatiing the contribution of each node to its community's modularity, [(Platig et al. 2016)]) This function uses the result of PANDA algorithm as the input dataset to run CONDOR algorithm. More about condor package and usage.
Arguments
- panda.net
Data Frame indicating the result of PANDA regulatory network, created by
pandaPy- threshold
Numeric vector of the customered threshold to select edges. Default value is the the midpoint between the median edge-weight of prior ( 3rd column "Motif" is 1.0) edges and the median edge-weight of non-prior edges (3rd column "Motif" is 0.0) in PANDA network. and the median edge-weight of non-prior edges (3rd column "Motif" is 0.0) in PANDA network.
Value
a CONDOR object, see createCondorObject.
Examples
# refer to three input datasets files in inst/extdat
treated_expression_file_path <- system.file("extdata", "expr4_matched.txt",
package = "netZooR", mustWork = TRUE)
motif_file_path <- system.file("extdata", "chip_matched.txt", package = "netZooR", mustWork = TRUE)
ppi_file_path <- system.file("extdata", "ppi_matched.txt", package = "netZooR", mustWork = TRUE)
# Run PANDA to construct the treated network
# \donttest{
treated_all_panda_result <- pandaPy(expr_file = treated_expression_file_path,
motif_file= motif_file_path, ppi_file = ppi_file_path,
modeProcess="legacy", remove_missing = TRUE )
# access PANDA regulatory network
treated_net <- treated_all_panda_result$panda
# Obtain the condor.object from PANDA network
treated_condor_object <- pandaToCondorObject(treated_net, threshold = 0)
# cluster condor.object
treated_condor_object <- condorCluster(treated_condor_object, project = FALSE)
# package igraph and package viridisLite are already loaded with this package.
library(viridisLite)
treated_color_num <- max(treated_condor_object$red.memb$com)
treated_color <- viridis(treated_color_num, alpha = 1, begin = 0, end = 1,
direction = 1, option = "D")
condorPlotCommunities(treated_condor_object, color_list=treated_color,
point.size=0.04, xlab="Target", ylab="Regulator")
# }