Getting data from TOM matrix (WGCNA)

Hello,

I would like to access the correlation in TOM matrix of a specific subset of genes. Manually, as it is a matrix, there’re no row/column names so I can’t identify the genes I’m looking for.

In the manual, I’ve seen the function

```
subsetTOM(
datExpr,
subset,
corFnc = "cor", corOptions = "use="p"",
weights = NULL,
networkType = "unsigned",
power = 6,
verbose = 1, indent = 0)
```

but I couldn’t figure out what is the “subset” object and haven’t found anything online either. It is described as

a single logical or numeric vector giving the indices of the nodes for

which the TOM is to be calculated

Is it a vector of Trues and Falses for each gene, being True the ones I am looking for?

• 18 views

Read more here: Source link