wTO.export: wTO.export

In wTO: Computing Weighted Topological Overlaps (wTO) & Consensus wTO Network

wTO.export

Description

Exports the significative interactions, the wTO weight and pvalues into a .txt file, tab separeted. This file can be imported in other visualization tools (Cytoscape for example).

Usage

wTO.export(DATA, path, sign = TRUE, pvalue = 0.05, padj = 0.05, prop.NA = 0.5)

Arguments

DATA	Output from the function wTO.Complete or wTO.Consensus.
path	Path and file name where the .txt file should be saved.
sign	Should the network contain the results for the signed network or unsigned? Only for data coming from wTO.Complete.
pvalue	cutoff p-value for the network. Only for data coming from wTO.Complete.
padj	cutoff adjusted p-value for the network. Only for data coming from wTO.Complete.
prop.NA	cutoff proportion of NAs for the network. Only for data coming from wTO.Consensus.

Examples

## Not run: 
EXAMPLE =  wTO.Complete( k =1, n = 200, Data = Microarray_Expression2,
                                      Overlap = ExampleGRF$x, method = "p")
wTO.export(EXAMPLE , './EXAMPLE.txt')

#Selection of only the significative ones for the Consensus
Ex_k1_cor_p_boot_p005_sig = subset(EXAMPLE$wTO,
EXAMPLE$wTO$pval_sig < 0.05,
select = c("Node.1", "Node.2", "wTO_sign"))
Ex_k1_cor_p_boot_p005_abs = subset(EXAMPLE$wTO,
EXAMPLE$wTO$pval_abs < 0.05,
select = c("Node.1", "Node.2", "wTO_abs"))
# Constructing the consensus network
CN = wTO.Consensus(data = list(Ex_k1_cor_p_boot_p005_sig,
Ex_k1_cor_p_boot_p005_abs))
wTO.export(CN, './CN.txt')
### You can store the result on the workspace.
y = wTO.export(CN, './CN.txt')
head(y)

## End(Not run)

wTO documentation built on Sept. 11, 2024, 6:21 p.m.