import.net: Import a network text file

In NEArender: Network Enrichment Analysis

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

import.net(tbl, Lowercase = 1, col.1 = 1, col.2 = 2, col.score = 3,
  min.score = NA, n.top = NA, 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).
col.score	Number of column where edge confidence score is found.
min.score	Minimum confidence score for an edge to be included in the network.
n.top	Number of edges to be included in the network, top when ranked by confidence score (is alternative to min.score).
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

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

NEArender documentation built on May 2, 2019, 8:30 a.m.