undefined arguments in blockwiseConsensusModules

[Bisho2122]

I don't see the arguments scaleTOMs, scaleQuantile, and sampleForScaling in WGCNA::blockwiseConsensusModules. Don't you mean the following params :

 networkCalibration = c("single quantile", "full quantile", "none"),

 # Simple quantile calibration options

 calibrationQuantile = 0.95,
 sampleForCalibration = TRUE, sampleForCalibrationFactor = 1000,
 getNetworkCalibrationSamples = FALSE`

It seems to be working fine, but I don't see these arguments are being used while debugging WGCNA::blockwiseConsensusModules.

https://github.com/smorabit/hdWGCNA/blob/6cc1546c37e1ae1ed3798ae90b0d75a425aa74b3/R/ConstructNetwork.R#L39

[smorabit]

Thanks for pointing this out. It looks like these arguments are used in older versions of WGCNA. For example see the documentation of this function in version 1.2. I am not sure exactly when it changed.

Later this week I will update ConstructNetwork with the correct parameter names, and enforce the appropriate version of WGCNA as a dependency.

[Bisho2122]

Thanks for the clarification and sharing the older version. I didn't see this one.

Feel free to close the issue whenever you update it. I think I made it work internally by providing the updated arguments and it worked.

Thanks again for providing the package, I am having a lot of fun with it :)

[smorabit]

These parameters have been fixed in the newest version of hdWGCNA.