pandaToCondorObject: Turn PANDA network into a CONDOR object

In netZoo/netZooR: Unified methods for the inference and analysis of gene regulatory networks

Turn PANDA network into a CONDOR object

Description

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.

Usage

pandaToCondorObject(panda.net, threshold)

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

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")

netZoo/netZooR documentation built on Oct. 16, 2024, 10:23 p.m.