MS_tissueFilter {MetaboSignal} | R Documentation

## Filter network based on tissue expression data

### 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")

[Package MetaboSignal version 1.24.0 Index]