Package index • PTMsToPathways

All functions

BuildClusterFilteredNetwork(): Build PPI Network
BuildPathwayCrosstalkNetwork(): Build Pathway Crosstalk Network
EvaluateClusters(): Evaluate Cluster Quality from PTM Data
GetGeneMANIA.edges(): Get GeneMANIA Edges
GetKinsub.edges(): Get Kinase-Substrate Edges
GetSTRINGdb.edges(): Get STRINGdb PPI data from full local or live source
GraphCfn(): Graph a Cluster Filtered Network in Cytoscape
MakeClusterList(): Build Clusters Based on PTM Data Under Like Conditions
MakeCorrelationNetwork(): Make Correlation Network
MakeDBInput(): Make Database Input File
NodeEdgeKey(): Create a node and edge legend network in Cytoscape
PTMsToPathways-package PTMsToPathways: PTMsToPathways: Filtered CoCluster Correlation Network Guide
ReadBioplanetFile(): Read Bioplanet File
StandardizeGeneSymbols(): Standardize Gene Symbols
connectNodes.all(): Connect a pair of nodes via all shortest paths
cytoscape.graph.PCN.pathways(): Graph a Pathway Crosstalk Network in Cytoscape
filter.edges.0(): Filter an edge file to edges between a specified set of nodes
filter.edges.1(): Filter an edge file to include first-order neighbours of specified nodes
filter.edges.between(): Filter an edge file to edges between two sets of nodes
fix.excel(): Correct Excel-Converted Gene Symbols
function_key: Function Key Example
get.co.clustered.ptms(): Retrieve co-clustered PTM CCCN edges for genes in an edge file
getCyEdgeNames(): Get Cytoscape-formatted edge names
`%w/o%`: Set difference for vectors using custom infix operator
graph.ptm.by.cluster(): Heatmap of Phosphopeptides Grouped by Cluster
harmonize_cfs(): Harmonize gene and PTM node tables for a combined CFN/CCCN network
make.cytoscape.node.file(): Build a Cytoscape node attribute table from an edge file
make.gene.data.from.ptmtable(): Summarise PTM table data to gene level
make.genepep.edges(): Create gene-to-peptide edges from a PTM edge file
merge2cols(): Merge Technical Replicate Values
mergeEdges(): Merge duplicate edges in an edge file
name.peptide(): Create PTM Peptide Names
outersect(): Symmetric set difference of two vectors
ptms_to_cfn(): Extracts co-clustered PTM and gene network from a cluster filtered network object.
remove.autophos(): Remove self-loop edges from an edge file
setCorrEdgeAppearance(): Apply edge visual mappings in the active Cytoscape network
setEdgeWidths(): Adjust edge line widths in the active Cytoscape network
setNodeColorToRatios(): Map node size and color to ratio-scale data in Cytoscape
setNodeColorToRowz(): Map node size and color to row z-score data in Cytoscape
setNodeMapping(): Apply node visual mappings in the active Cytoscape network
setNodeSizeColorIndependently(): Set node size and color from independent Cytoscape node attributes
strip.cy.goo(): Strip Cytoscape metadata strings to extract node names