Fig. 1
The wTO package workflow. Gray boxes refer to inputs, red boxes refer to content of the wTO package, yellow boxes are functions included in the package, blue boxes are outputs of those functions, and green boxes refer to methods internal to the package. Our package can deal with multiple kinds of data, for example RNA-seq counts or normalized values, microarray expression data, abundance data coming from metagenomic studies, and many more. All input data should be pre-processed with the quality control and normalization methods recommended for each respective type of data. The function wTO.Complete calculates the wTO values, as many times as desired. As output, the user will obtain an object containing the signed and absolute wTO values for each pair of nodes, p-values and padj-values for multiple testing. This output can be used for the construction of a CN from independent networks using the function wTO.Consensus. Outputs from the wTO and CN networks can be used as an input for NetVis, which is an integrated tool for plotting networks. As an interactive tool it also allows the user to modify the network