Network Analysis for MS-based Proteomics Experiments

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Documentation for package ‘MSstatsBioNet’ version 1.5.4

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

.validateAnnotateProteinInfoFromIndraInput	Validate Annotate Protein Info Input
annotateProteinInfoFromIndra	Annotate Protein Information from Indra
backend_capabilities	What a backend supports
backend_capabilities-method	What a backend supports
bootstrapTopicModels	Bootstrap the topic decomposition to find each topic's robust top words
compareTopicModels	Test whether including PPIs changes topic structure beyond random chance
convert_ids	Ground entities in a backend's namespaces
convert_ids-method	Ground entities in a backend's namespaces
cytoscapeNetwork	Render a Cytoscape network visualisation
cytoscapeNetworkOutput	Shiny output binding for cytoscapeNetwork
decomposeSubnetworkByTopic	Decompose a subnetwork into topic-specific subnetworks via joint NMF
decomposeSubnetworkIntoHierarchicalTopics	Recursively decompose a subnetwork into a hierarchy of topic subnetworks
deleteEdgeFromNetwork	Delete an edge from a network edges data frame
exportNetworkToHTML	Export network data with Cytoscape visualization
filterSubnetworkByContext	Filter a subnetwork by contextual relevance
filter_by_curation	Remove evidence curated as incorrect
getSubnetworkFromIndra	Get subnetwork from INDRA database
get_curations	Get the curations of edges from a backend
get_curations-method	Get the curations of edges from a backend
get_entity_properties	Add a backend's properties of each entity
get_entity_properties-method	Add a backend's properties of each entity
get_evidence	Get the evidence behind network edges
get_evidence-method	Get the evidence behind network edges
get_network	Get a network from a backend
get_network-method	Get a network from a backend
IndraBackend-class	Network backend classes
indra_backend	Create an INDRA backend
INDRA_DATABASE_SOURCES	Evidence sources of INDRA
indra_evidence_sources	Evidence sources of INDRA
INDRA_TEXT_MINED_SOURCES	Evidence sources of INDRA
load_network	Load a network saved with save_network()
merge_networks	Combine networks from several queries or backends
NetworkBackend-class	Network backend classes
NetworkQuery-class	Network query classes
network_queries	Questions you can ask of a network backend
prepare_entities	Prepare an entity table from MSstats results
previewNetworkInBrowser	Preview network in browser
print.topicHierarchy	Print a topic hierarchy as an indented tree
renderCytoscapeNetwork	Render a Cytoscape network in a Shiny application. This function is used to render a Cytoscape network visualization within a Shiny application.
save_network	Save a network to a file
select_entities	Flag the entities to query
SubnetworkQuery-class	Network query classes
subnetwork_query	How are my selected entities connected to each other?
validate_network	Validate a network against the edge and node contract