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(): Format Kinsub Table
GetSTRINGdb.edges(): Get STRINGdb PPI data
MakeClusterList(): Build Clusters Based on PTM Data Under Like Conditions
MakeCorrelationNetwork(): Make Correlation Network
MakeDBInput(): Make Database Input File
ex_pathways_list: Pathways list
fix.excel(): Correct Excel-Converted Gene Symbols
getFuncKey(): Graphing and Manipulating Cluster Filtered Network
`%w/o%`: Set difference for vectors using custom infix operator
graph.ptm.by.cluster(): Heatmap of Phosphopeptides Grouped by Cluster
make.genepep.edges(): Title
merge2cols(): Merge Technical Replicate Values
name.peptide(): Create PTM Peptide Names
ptms_to_cfn(): Extracts co-clustered PTM and gene network from a cluster filtered network object.
remove.autophos(): Title
setCorrEdgeAppearance(): Title
setNodeSizeColorIndependently(): Set node size and color from independent Cytoscape node attributes