runPanda: Run pypanda in R

In twangxxx/netZoo: Integrate methods: PANDA, LIONESS, CONDOR, ALPACA into one workflow.

Description

PANDA(Passing Attributes between Networks for Data Assimilation) is a message-passing model to gene regulatory network reconstruction. It integrates multiple sources of biological data, including protein-protein interaction, gene expression, and sequence motif information, in order to reconstruct genome-wide, condition-specific regulatory networks. [(Glass et al. 2013)]) This function is able to run pypanda – Python implementation of PANDA in R enviroment.

Usage

runPanda(e = expression, m = motif, ppi = ppi, rm_missing = FALSE)

Arguments

e	Character String indicatining the file path of expression values file, as each gene (row) by samples (columns) required
m	Character String indicatining the file path of pair file of motif edges, when not provided, analysis continues with Pearson correlation matrix. optional
ppi	Character String indicatining the pair file path of Protein-Protein interaction dataset. optional
rm_missing	Boolean indicatining whether to remove missing values. If TRUE, removes missing values. if FALSE, keep missing values. THe default value is FALSE. optional

Value

List of three items<ef><bc><9a> Use $panda to access the entire data frame of PANDA output network consisting of four columns: "tf", "gene", "motif", and "force".

Use $indegree to access the data frame of indegree of PANDA network, consisting of two columns: "gene", "force".

Use $outdegree to access the data frame of outdegree of PANDA network, consisting of two columns: "tf", "force".

Note: If there is any duplicate name of nodes in first two columns, prefix the content in regulator column with "reg_" and content in target column with"tar_"

Please re-name the colnames if needed.

Examples

# refer to four input datasets files in inst/extdat
treated_expression_file_path <- system.file("extdata", "expr4.txt", package = "netZoo", mustWork = TRUE)
control_expression_file_path <- system.file("extdata", "expr10.txt", package = "netZoo", mustWork = TRUE)
motif_file_path <- system.file("extdata", "chip.txt", package = "netZoo", mustWork = TRUE)
ppi_file_path <- system.file("extdata", "ppi.txt", package = "netZoo", mustWork = TRUE)


# Run PANDA for treated and control network
treated_all_panda_result <- runPanda(e = treated_expression_file_path, m = motif_file_path, ppi = ppi_file_path, rm_missing = TRUE )
control_all_panda_result <- runPanda(e = control_expression_file_path, m = motif_file_path, ppi = ppi_file_path, rm_missing = TRUE )

# access PANDA regulatory network
treated_net <- treated_all_panda_result$panda
control_net <- control_all_panda_result$panda

# access PANDA regulatory indegree network result
indegree_net <- treated_all_panda_result$indegree

# access PANDA regulatory outdegree network result
outdegree_net <- treated_all_panda_resultt$outdegree

twangxxx/netZoo documentation built on May 17, 2019, 1:02 p.m.