testMotif {pandaR} | R Documentation |
This function adds random false positive edges to the regulatory prior and will check if they become pruned.
testMotif(x, motif, expr, ppi, mode = c("augment", "remove"), prop = 0.05, seed = 1, ...)
x |
Model regulatory network. |
motif |
Motif used to construct the model regulatory network. |
expr |
Expression matrix used to construct model network. |
ppi |
PPI used to construct model regulatory network. |
mode |
a character string - either "augment" to add random edges or "remove" to remove random edges. |
prop |
numeric specifying number of edges to augment or remove from regulatory prior, as a proportion of the number of edges in the regulatory prior. |
seed |
Random seed. |
... |
Options for the panda function. |
ggplot heatmap list of indices of net corresponding to each TF
data(pandaToyData) data(pandaResult) regnet = slot(pandaResult,"regNet") with(pandaToyData, testMotif(regnet, motif, mode="augment", expression, ppi, hamming=1))