run_bc3net: Wrapper for BC3Net method

Description Usage Arguments Value References See Also Examples

View source: R/methods.R

Description

Conducts co-expression analysis using BC3Net \insertCitematos12dnapath. Uses the implementation from the bc3net package \insertCitebc3netdnapath. Can be used for the network_inference argument in dnapath.

Usage

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run_bc3net(
  x,
  boot = 100,
  estimator = "spearman",
  disc = "equalwidth",
  mtc1 = TRUE,
  adj1 = "bonferroni",
  alpha1 = 0.05,
  mtc2 = TRUE,
  adj2 = "bonferroni",
  alpha2 = 0.05,
  ...
)

Arguments

x

A n by p matrix of gene expression data (n samples and p genes).

boot

Argument is passed into bc3net.

estimator

Argument is passed into bc3net.

disc

Argument is passed into bc3net.

mtc1

Argument is passed into bc3net.

adj1

Argument is passed into bc3net.

alpha1

Argument is passed into bc3net.

mtc2

Argument is passed into bc3net.

adj2

Argument is passed into bc3net.

alpha2

Argument is passed into bc3net.

...

Additional arguments are ignored.

Value

A p by p matrix of association scores.

References

\insertRef

matos12dnapath

\insertRef

bc3netdnapath

See Also

run_aracne, run_c3net, run_clr, run_corr, run_dwlasso, run_genie3, run_glasso, run_mrnet, run_pcor, and run_silencer

Examples

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data(meso)
data(p53_pathways)

# To create a short example, we subset on one pathway from the p53 pathway list,
# and will only run 1 permutation for significance testing.
pathway_list <- p53_pathways[13]
n_perm <- 1

# Use this method to perform differential network analysis.
# The parameters in run_bc3net() can be adjusted using the ... argument.
# For example, the 'estimator' and 'boot' parameter can be specified as shown here.
results <- dnapath(x = meso$gene_expression,
                   pathway_list = pathway_list,
                   groups = meso$groups,
                   n_perm = n_perm,
                   network_inference = run_bc3net,
                   boot = 10,
                   estimator = "pearson",
                   mtc1 = FALSE,
                   mtc2 = FALSE)
summary(results)

# The group-specific association matrices can be extracted using get_networks().
nw_list <- get_networks(results) # Get networks for pathway 1.


# nw_list has length 2 and contains the inferred networks for the two groups.
# The gene names are the Entrezgene IDs from the original expression dataset.
# Renaming the genes in the dnapath results to rename those in the networks.
# NOTE: The temporary directory, tempdir(), is used in this example. In practice,
#       this argument can be removed or changed to an existing directory
results <- rename_genes(results, to = "symbol", species = "human",
                        dir_save = tempdir())
nw_list <- get_networks(results) # The genes (columns) will have new names.

# (Optional) Plot the network using SeqNet package (based on igraph plotting).
# First rename entrezgene IDs into gene symbols.
SeqNet::plot_network(nw_list[[1]])

dnapath documentation built on Dec. 11, 2021, 9:54 a.m.