MS_tissueFilter: Filter network based on tissue expression data

In MetaboSignal: MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways

Description

This function allows filtering a network based on tissue expression data from the Human Protein Atlas, by removing signaling genes that are not detected in the target tissue(s) (reliability = "approved" or "supported"). This function can be only used to filter human networks.

Usage

MS_tissueFilter(network_table, tissue, input_format = "kegg", expand_genes = FALSE)

Arguments

network_table	three-column matrix where each row represents an edge between two nodes. The gene nodes of this network must be human specific gene IDS (not orthologies). For this, use the function "MS_keggNetwork( )" with expand_genes = TRUE.
tissue	character vector indicating the tissue(s) of interest. Signaling genes (i.e. non-enzymatic genes) not detected in the target tissue(s) (reliability = "approved" or "supported") will be removed from the network. Check all possible tissues in the "hpaNormalTissue" dataset.
input_format	character vector indicating the gene format in the input network_table ("entrez" or "kegg").
expand_genes	logical scalar indicating whether the gene nodes in the filtered network will represent orthology IDs (expand_genes = FALSE) or organism-specific gene IDs (expand_genes = TRUE).

Value

A three-column matrix where each row represents an edge between two nodes.

References

Gatto, L. hpar: Human Protein Atlas in R.R package version 1.12.0.

http://www.kegg.jp/kegg/docs/keggapi.html

Examples

# Build network

net <- MS_keggNetwork(metabo_paths = "hsa00010", signaling_paths = "hsa04014",
                      expand_genes = TRUE)

# Filter network by liver and cluster genes by orthology

net_filtered <- MS_tissueFilter(net, tissue = "liver")

MetaboSignal documentation built on Nov. 8, 2020, 6 p.m.