pandaR (version 1.4.2)

testMotif: 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))