testMotif: Check motif

Description Usage Arguments Value Examples

Description

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

Usage

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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

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


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