wTO.Complete arguments / biological replicates

Question

[annaA]

Hello,

Currenlty I am working with RNA seq data from iPS cells ( 7 replicates for each day of differentiation, from day0 to day 4) and now I am on the step in which I wan to build the networks ( one for each day). To do so , I am using the wTO package. 1.I need to ask because it's not super clear to me , How I am gonna use the replicates for each day in the functions ? 2.I am running the wTO.Complete function with resampling method "Bootstrap" and I want to run in parallel . How i decide the number of threads (k) and amount of replications (n)?

 wTOs_p_signs_complete=wTO.Complete(k=5, n=250, Data = data_0dpi, Overlap = overlap$x, method='s', method_resampling="Bootstrap", pvalmethod="BH", savecor=TRUE, expected.diff= 0.2, plot=TRUE)

Data= data_0dpi contains all the data from the 7 biological replicates from day 0

Thanks for your help, Anna