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

Documentation for package ‘MetaboSignal’ version 1.4.0

directionality_reactions	List of KEGG reactions with incorrect/inconsistent directionality
hpaNormalTissue	Expression profiles for proteins in human tissues
MetaboSignal_distances	Calculate gene-metabolite distance matrix
MetaboSignal_matrix	Build MetaboSignal network-table
MetaboSignal_NetworkCytoscape	Build shortest-path subnetwork
MetaboSignal_table	Example of MetaboSignal network-table filtered by tissue expression
MetaboSignal_tableUnfiltered	Example of MetaboSignal network-table unfiltered by tissue expression
MS_ChangeNames	Transform KEGG IDs into common names
MS_FilterNetwork	Filter network based on distances or betweenness
MS_FindKEGG	Get KEGG IDs for compounds, organisms or pathways
MS_FindMappedNodes	Map gene IDs or metabolite IDs onto the network
MS_GetKEGG_GeneID	Transform entrez IDs or gene symbols into KEGG IDs
MS_GetShortestpaths	Calculate shortest paths
MS_NodeBW	Get distribution of node betweeness
MS_RemoveNode	Remove undesired nodes from the network
MS_ReplaceNode	Replace nodes of the network
MS_ToCytoscape	Export network in cytoscape format
neglected_genes	Genes removed during tissue-expression filtering
subnetwork	Shortest-path subnetwork