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goProfiles (version 1.34.0)

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

Description

The package implements methods to compare lists of genes based on comparing the corresponding 'functional profiles'.

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Version

Version

1.34.0

License

GPL-2

Maintainer

Alex Sanchez

Last Published

February 15th, 2017

Functions in goProfiles (1.34.0)

expandedLevel

Function to create expanded levels which can contain GO Terms at different GO levels
contractedProfile

Converts an expanded GO profile into a basic (contracted) GO profile
goProfiles-package

Performs Gene Ontology based analysis using Functional Profiles.
conversionFunctions

Functions to transformconvert objects between different types
compSummary

This function returns a brief summary of the comparison between two (expanded) profiles.
omimIds

Entrez identifiers for disease-related genes in the OMIM database
equivSummary

This function returns a brief summary of the equivalence test between two profiles.
CD4Ids

Entrez identifiers for CD4-TCells example
basicProfile

Builds basic functional profile
GOTermsList

Functions to create and manage lists of GO terms associated with a vector of 'Entrez' identifiers
compareProfilesLists

Compares two of expanded profiles
drosophila

Entrez identifiers for genes related with an eye mutation in drosophila
compareGeneLists

Compares two lists of genes by building (expanded) profiles and comparing them
compareGOProfiles

Comparison of lists of genes through their functional profiles
fitGOProfile

Does a "sample" GO profile 'pn', observed in a sample of 'n' genes, fit a "population" or "model" p0?
equivalentGOProfiles

Are two lists of genes equivalent in terms of their Gene Ontology profiles?
printProfiles

Print functional profiles
hugoIds

Entrez Identifiers obtained from the Human Genome Organization
plotProfiles

Plot functional profiles
prostateIds

Prostate cancer-related genes
expandedProfile

Builds expanded profiles
ngenes

Returns the number of genes that lead to this GO profile (an object of class ExpandedGOProfile, BasicGOProfile or assimilable to them)
mergeProfilesLists

Combines two lists of profiles into one
fisherGOProfiles

GO Class-by-class Fisher tests in lists of genes characterized by their functional profiles