gx.searchRegulators: Regulator search
In genexplain/geneXplainR: An R interface for the geneXplain platform

gx.searchRegulators

R Documentation

Regulator search

Description

Searches for signal transduction regulators of input proteins

Usage

gx.searchRegulators(sourcePath, weightColumn, limitInputSize = FALSE,
  inputSizeLimit = 1000, maxRadius = 5, scoreCutoff = 0.2, bioHub,
  species = "Human (Homo sapiens)", calculateFdr = TRUE,
  fdrCutoff = 0.05, zscoreCutoff = 1, penalty = 0.1,
  isoformFactor = TRUE, contextDecorators = c(),
  removeNodeDecorators = c(), outputTable, wait = TRUE,
  verbose = TRUE)

Arguments

`sourcePath`	Path of table with input protein/molecule set
`weightColumn`	Name of column in input table with weights (optional)
`limitInputSize`	True to take only the first N inputs
`inputSizeLimit`	Number of inputs to use from input table
`maxRadius`	Max. number of reactions/interactions to connect inputs to regulators
`scoreCutoff`	Cutoff for regulator score
`bioHub`	Molecular network database to use
`species`	Species whose network shall be analyzed
`calculateFdr`	True to create random inputs for Z-score calculation
`fdrCutoff`	Cutoff to consider regulators significant
`zscoreCutoff`	Cutoff for Z-score
`penalty`	Penalty for non-input hits in regulator network
`isoformFactor`	Normalize multi-forms
`contextDecorators`	List of lists with context decorator parameters like list('A'=list(table='table path', column='column name', 'decay'=<value>), list(), ...)
`removeNodeDecorators`	List of table paths specifying nodes to remove
`outputTable`	Path to store analysis results
`wait`	True to wait for job to complete
`verbose`	True for more progress info