goProfiles: an R package for the statistical analysis of functional profiles


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Documentation for package ‘goProfiles’ version 1.12.0

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goProfiles-package Performs Gene Ontology based analysis using Functional Profiles.
as.GOTerms.frame Functions to transformconvert objects between different types
as.GOTerms.list Functions to transformconvert objects between different types
basicProfile Builds basic functional profile
BioCpack2EntrezIDS Functions to transformconvert objects between different types
BioCpack2Profiles Functions to transformconvert objects between different types
BioCprobes2Entrez Functions to transformconvert objects between different types
CD4GOTermsFrame Entrez identifiers for CD4-TCells example
CD4GOTermsList Entrez identifiers for CD4-TCells example
CD4LLids Entrez identifiers for CD4-TCells example
compareGeneLists Compares two lists of genes by building (expanded) profiles and
compareGOProfiles Comparison of lists of genes through their functional profiles
compareProfilesLists Compares two of expanded profiles
compSummary This function returns a brief summary of the comparison between two
contractedProfile Converts an expanded GO profile into a basic (contracted) GO profile
contractedProfile.default Converts an expanded GO profile into a basic (contracted) GO profile
contractedProfile.ExpandedGOProfile Converts an expanded GO profile into a basic (contracted) GO profile
diseaseIds Entrez identifiers for disease-related genes in the OMIM database
dominantIds Entrez identifiers for disease-related genes in the OMIM database
dominantIdsEBI Entrez identifiers for disease-related genes in the OMIM database
dominantIdsNCBI Entrez identifiers for disease-related genes in the OMIM database
drosophilaIds Entrez identifiers for genes related with an eye mutation in drosophila
equivalentGOProfiles Are two lists of genes equivalent in terms of their Gene Ontology
equivalentGOProfiles.default Are two lists of genes equivalent in terms of their Gene Ontology
equivalentGOProfiles.ExpandedGOProfile Are two lists of genes equivalent in terms of their Gene Ontology
equivalentGOProfiles.GOProfileHtest Are two lists of genes equivalent in terms of their Gene Ontology
equivalentGOProfiles.list Are two lists of genes equivalent in terms of their Gene Ontology
equivSummary This function returns a brief summary of the equivalence test between
expandedLevel Function to create expanded levels which can contain GO Terms at
expandedProfile Builds expanded profiles
expandTerm Function to create expanded levels which can contain GO Terms at
fisherGOProfiles GO Class-by-class Fisher tests in lists of genes characterized by their
fisherGOProfiles.BasicGOProfile GO Class-by-class Fisher tests in lists of genes characterized by their
fisherGOProfiles.ExpandedGOProfile GO Class-by-class Fisher tests in lists of genes characterized by their
fisherGOProfiles.matrix GO Class-by-class Fisher tests in lists of genes characterized by their
fisherGOProfiles.numeric GO Class-by-class Fisher tests in lists of genes characterized by their
fitGOProfile Does a "sample" GO profile 'pn', observed in a sample of 'n' genes, fit
getAncestorsLst Functions to create and manage lists of GO terms associated with a
getGOLevel Functions to create and manage lists of GO terms associated with a
goProfiles Performs Gene Ontology based analysis using Functional Profiles.
GOTermsFrame2GOTermsList Functions to transformconvert objects between different types
GOTermsList Functions to create and manage lists of GO terms associated with a
hugoIds Entrez Identifiers obtained from the Human Genome Organization
mergeProfilesLists Combines two lists of profiles into one
michaudIds Entrez identifiers for genes related with an eye mutation in drosophila
morbidmapIds Entrez identifiers for disease-related genes in the OMIM database
ngenes Returns the number of genes that lead to this GO profile (an object of
ngenes.BasicGOProfile Returns the number of genes that lead to this GO profile (an object of
ngenes.default Returns the number of genes that lead to this GO profile (an object of
ngenes.ExpandedGOProfile Returns the number of genes that lead to this GO profile (an object of
ngenes.matrix Returns the number of genes that lead to this GO profile (an object of
ngenes.numeric Returns the number of genes that lead to this GO profile (an object of
omimIds Entrez identifiers for disease-related genes in the OMIM database
ostrinIds Entrez identifiers for genes related with an eye mutation in drosophila
plotProfiles Plot functional profiles
printProfiles Print functional profiles
prostateIds Prostate cancer-related genes
recessiveIds Entrez identifiers for disease-related genes in the OMIM database
recessiveIdsEBI Entrez identifiers for disease-related genes in the OMIM database
recessiveIdsNCBI Entrez identifiers for disease-related genes in the OMIM database
singh01EntrezIDs Prostate cancer-related genes
singh05EntrezIDs Prostate cancer-related genes
welsh01EntrezIDs Prostate cancer-related genes
welsh05EntrezIDs Prostate cancer-related genes