summaryTable: Main pathway analysis function.

In biodev/packageDir: Tool for in silico functional analysis design and exploration of relation between genomic function and aberration.

Description

The main function for conducting a pathway analysis on a set of gene data.

Usage

summaryTable(study, activeGeneDescription = "active_gene",
  dataSetDescription = "analysis of undefined active genes",
  pgm = NULL, originalDataMatrix = NULL,
  settings = getDefaultSettings()$defaultSummaryTable, coverage = NULL,
  coverageGeneDescription = "covered_gene",
  coverageDataSetDescription = "Coverage analysis",
  individualEnrichment = NULL)

Arguments

study	A Study object.
activeGeneDescription	One word description of how the 'active' genes should be described (ex: mutated, amplified, drug_sensitive)
dataSetDescription	Description of the data set provided for the pathway analysis. (ex: "Somatically mutated genes")
pgm	The patient gene matrix for the patient data. Bipartate graph with row names set as gene names, column names set as patient IDs and values logical indicating if gene is considered "active" in patient.
originalDataMatrix	The original data matrix. Makes this available for novel types of pathway analysis, not treating genes as discretely "on" or "off"
settings	A settings list object controling how the path analysis will be conducted. Default given by call to getDefaultSettings()$defaultSummaryTable .
coverage	character vector of gene names. Should be provided if coverage provided by the analysis platform used to produce gene data entered into this function is not considered to have full genome coverage.
coverageGeneDescription	The description of genes that are covered be the analysis platform (ex: drug_targeted or sequenced)
coverageDataSetDescription	A longer description of the set of genes provided in the coverage analysis
individualEnrichment	logical. A flag indicating if pathway analysis should be run for individual patients.

Examples

studyObject = getStudyObject(study.name="testStudy", path_detail=getDefaultPaths())

#conduct an analysis of pathway coverage only. 
targetlist  = c("NT5C2", "GUK1",  "ADAL",  "PCK1")
coverageAnalysis = summaryTable(study=studyObject, 
				coverageGeneDescription="testCoverageGene", 
				coverageDataSetDescription="test coverage analysis", 
				coverage=targetlist)

#conduct full pathway analysis
pathwayAnalysis = summaryTable(study=studyObject, 
															pgm=getTestPGM(),
															dataSetDescription="test analysis of gene data",
															activeGeneDescription="analyzed_gene")
## Not run: 
View(pathwayAnalysis$patientsums)

## End(Not run)

biodev/packageDir documentation built on Nov. 4, 2019, 7:19 a.m.