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


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Documentation for package ‘goProfiles’ version 1.2.0

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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
basicCD4 Sample Profiles computed on some datasets in the package
basicHugo Sample Profiles computed on some datasets in the package
basicProfile Builds basic functional profile
basicSingh01 Sample Profiles computed on some datasets in the package
basicWelsh01 Sample Profiles computed on some datasets in the package
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
commonExpandedWelsh01Singh01 Sample Profiles computed on some datasets in the package
compareGeneLists Compares two lists of genes by building (expanded) profiles and comparing them
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 (expanded) profiles.
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 profiles?
equivSummary This function returns a brief summary of the equivalence test between two profiles.
expandedCD4 Sample Profiles computed on some datasets in the package
expandedHugo Sample Profiles computed on some datasets in the package
expandedLevel Function to create expanded levels which can contain GO Terms at different GO levels
expandedProfile Builds expanded profiles
expandedSingh01 Sample Profiles computed on some datasets in the package
expandedWelsh01 Sample Profiles computed on some datasets in the package
expandTerm Function to create expanded levels which can contain GO Terms at different GO levels
fitGOProfile Does a "sample" GO profile 'pn', observed in a sample of 'n' genes, fit a "population" or "model" p0?
getAncestorsLst Functions to create and manage lists of GO terms associated with a vector of 'Entrez' identifiers
getGOLevel Functions to create and manage lists of GO terms associated with a vector of 'Entrez' identifiers
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 vector of 'Entrez' identifiers
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
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
sampleProfiles Sample Profiles computed on some datasets in the package
singh01EntrezIDs Prostate cancer-related genes
singh05EntrezIDs Prostate cancer-related genes
welsh01EntrezIDs Prostate cancer-related genes
welsh05EntrezIDs Prostate cancer-related genes