testMotif: Check motif

In jnpaulson/pandaR: PANDA Algorithm

Check motif

Description

This function adds random false positive edges to the regulatory prior and will check if they become pruned.

Usage

testMotif(
  x,
  motif,
  expr,
  ppi,
  mode = c("augment", "remove"),
  prop = 0.05,
  seed = 1,
  ...
)

Arguments

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.

Value

ggplot heatmap list of indices of net corresponding to each TF

Examples

data(pandaToyData)
data(pandaResult)
regnet = slot(pandaResult,"regNet")
with(pandaToyData, testMotif(regnet, motif, mode="augment", expression, ppi, hamming=1))

jnpaulson/pandaR documentation built on Oct. 1, 2023, 3:14 a.m.