tutorial please!

[kieran-mace]

Not sure how to get started with this. Can you make a minimal script that steps through a regular workflow?

[nishagove]

Yeah. Looking forward to a tutorial. I find it rather confusing especially when the file labels of each function don't match with the other. For example, the function 1 generates an output that would serve as an input for function 2. I get lost when the names differ. A tutorial will certainly resolve all confusions.

[julipetal]

I am sorry for the delay - I needed a break from the computer and drove across country and disconnected.

You only really have to call one function
dataToVNs(dataFile, GoIFile, annoFile, metric, thresholds, MMoExists)

dataFile is your gene expression file in tab-separated .txt format, rows are individual genes and columns are conditions/measurements
GoIFile is another tab (or line)-separated .txt file including genes that are of interest to you

all other inputs are optional
annoFile stands for annotation file. If you have an annotation file for your genes (or whatever your node definition is), this file can be uploaded as well and then the groups (vicinity networks) will be annotated. This file can include anything you want, it just needs to be a tab-separated .txt file and the first column needs to include (not all or more) gene identifies matching the ones from the expression input file
metric is the association measure used to define edges between nodes, default is Spearman. The association measure can be set to other correlation or distance measures, if you are working with RNAseq - I recommend leaving it as is
thresholds is a numeric vector indicating where to cut of the weight for the edges, I recommend not to specify values, the program will calculate the best thresholds
MMoExists can be ignored

so your function call could look something like this
dataToVNs("myDataFile.txt", "myGenesOfInterest.txt")
OR
dataToVNs("myDataFile.txt", "myGenesOfInterest.txt", "myAnnotationFile.txt")