WGCNA Eigengene and intramodularConnectivity
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Entering edit mode
2.2 years ago
AJ ▴ 20

Im trying to get the genes that contribute to the 1st PC, i.e the Eigengene. For this im trying the following function:

https://www.rdocumentation.org/packages/WGCNA/versions/1.68/topics/intramodularConnectivity. There are two ways to execute this function:

1) use of the following syntax:

IntramodularConnectivity(adjMat, colors, scaleByMax = FALSE)

How would I get the adjacency matrix for this function?

2) use of the following syntax:

intramodularConnectivity.fromExpr(datExpr, colors, 
          corFnc = "cor", corOptions = "use = 'p'",
          weights = NULL,
          distFnc = "dist", distOptions = "method = 'euclidean'",
          networkType = "unsigned", power = if (networkType=="distance") 1 else 6,
          scaleByMax = FALSE,
          ignoreColors = if (is.numeric(colors)) 0 else "grey",
          getWholeNetworkConnectivity = TRUE)

keeps giving me the error:

"Error in intramodularConnectivity.fromExpr(datExpr = datModule_black, : Number of columns (genes) in 'datExpr' and length of 'colors' differ."

wgcna RNA-Seq network • 956 views
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How did you create datExpr and colors? - please confirm that you have followed the WGCNA vignettes / tutorials regarding how to properly create these objects.

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