Import a network text file

Description

This function reads in a TAB-delimited file with the global network data needed for NEA. Checks the format of the given NETWORK file, processes unique genes from the given network file, and counts the network links.

Usage

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import.net(tbl, Lowercase = 1, col.1 = 1, col.2 = 2, echo = 1)

Arguments

tbl

Input network file.

Lowercase

Render gene/protein IDs lower-case.

col.1

Number of the column in the input file that corresponds to node 1 (gene/protein ID).

col.2

Number of the column in the input file that corresponds to node 2 (gene/protein ID).

echo

if execution progress should be reported.

Value

$Ntotal, the total number of edges in the network and $links, an object with members (named by gene/protein IDs) that correspond to each node in the global network. Each entry of the list $links contains a vector of neighbours of the respective node.

See Also

mutations2ags, samples2ags

Examples

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data(net.kegg)
netpath <- net.kegg
net <- import.net(netpath)
summary(net$links)
print(paste(names(net$links)[100], net$links[[100]], sep=": "))