GOTermsList
(Package: goProfiles) :
Functions to create and manage lists of GO terms associated with a vector of 'Entrez' identifiers
These functions prepare data to be processed by the 'basicProfile' function. To create a profile a set of GOterms belonging to one or more ontologies is needed The terms belonging to each gene must be given separately so that they can be counted. This function queries the environment 'GOENTREZID2GO' with the vector of Entrez terms and formats the output into a list whose components -one per Entrez term- contain the most specific GO identifiers associated with this term.
● Data Source:
BioConductor
● Keywords: manip
● Alias: GOTermsList, getAncestorsLst, getGOLevel
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basicProfile
(Package: goProfiles) :
Builds basic functional profile
Compute basic functional profile for a given list of genes/GO identifiers, a given ontology at a given level of the GO
● Data Source:
BioConductor
● Keywords: htest
● Alias: basicProfile
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compSummary
(Package: goProfiles) :
This function returns a brief summary of the comparison between two (expanded) profiles.
Function to return a brief summary of the comparison between two (expanded) profiles.
● Data Source:
BioConductor
● Keywords: htest
● Alias: compSummary
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compareGOProfiles
(Package: goProfiles) :
Comparison of lists of genes through their functional profiles
Compare two samples of genes in terms of their GO profiles pn and qm. Both samples may share a common subsample of genes, with GO profile pqn0. 'compareGOProfiles' implements some inferential procedures based on asymptotic properties of the squared euclidean distance between the contracted versions of pn and qm
● Data Source:
BioConductor
● Keywords: htest
● Alias: compareGOProfiles
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compareGeneLists
(Package: goProfiles) :
Compares two lists of genes by building (expanded) profiles and comparing them
This function wraps all the needed steps to compare two lists of genes following the methodology developed by Sanchez, Salicru and Ocan~a (2007)
● Data Source:
BioConductor
● Keywords: htest
● Alias: compareGeneLists
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This function compares two lists (“sensu R lists”) of expanded profiles by successive calls to function compareGOProfiles following the methodology developed by Sanchez, Salicru and Ocan~a (2007)
● Data Source:
BioConductor
● Keywords: htest
● Alias: compareProfilesLists
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contractedProfile
(Package: goProfiles) :
Converts an expanded GO profile into a basic (contracted) GO profile
Converts an object of class 'ExpandedGOProfile', or assimilable to it, in an object of class 'BasicGOProfile'
● Data Source:
BioConductor
● Keywords:
● Alias: contractedProfile, contractedProfile.ExpandedGOProfile, contractedProfile.default
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conversionFunctions
(Package: goProfiles) :
Functions to transformconvert objects between different types
These functions transform data from one classtype into another, or pack simple processes such as compute the profiles needed for one annotations package.
● Data Source:
BioConductor
● Keywords: manip
● Alias: BioCpack2EntrezIDS, BioCpack2Profiles, BioCprobes2Entrez, GOTermsFrame2GOTermsList, as.GOTerms.frame, as.GOTerms.list
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equivSummary
(Package: goProfiles) :
This function returns a brief summary of the equivalence test between two profiles.
Function to return a brief summary of the equivalence test between two profiles. If In its current version it is better that equivalentGOProfiles is called with option simplify set to FALSE before equivSummary can be used
● Data Source:
BioConductor
● Keywords: htest
● Alias: equivSummary
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equivalentGOProfiles
(Package: goProfiles) :
Are two lists of genes equivalent in terms of their Gene Ontology profiles?
Performs an equivalence test based on the squared Euclidean distance between the Gene Ontology profiles of two lists of genes. Equivalence is declared if the upper limit d.sup of a one-sided confidence interval [0, d.sup] for the distance is lesser than the equivalence limit d0.
● Data Source:
BioConductor
● Keywords: htest
● Alias: equivalentGOProfiles, equivalentGOProfiles.ExpandedGOProfile, equivalentGOProfiles.GOProfileHtest, equivalentGOProfiles.default
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