Usage
basicProfile(genelist, idType = "Entrez", onto = "ANY", level = 2,orgPackage=NULL, anotPackage=NULL,
ord = TRUE, multilevels = NULL, empty.cats = TRUE, cat.names = TRUE, na.rm = TRUE)
Arguments
genelist
List of genes on which the Profile has to be based
idType
Type of identifiers for the genes. May be 'Entrez' (default), BiocProbes or GoTermsFrame (see details below).
onto
Ontology on which the profile has to be built
level
Level of the ontology at which the profile has to be
built
orgPackage
Name of a Bioconductor's organism annotations package
('org.Xx-eg-db'). This field must be provided if the gene list passed
to the function is either a character vector of 'Entrez' (NCBI) identifiers or a character vector of probe names
anotPackage
Name of Bioconductor's microarray annotations package. This field must be provided if the gene list passed to the function is a character vector of probe names
ord
Set to 'TRUE' if the profile has to appear ordered by the category names
multilevels
If it is not NULL it must be a vector of GO categories that defines the level at where the profile is built
empty.cats
Set to 'TRUE' if empty categories should appear in the profile
cat.names
Set to 'TRUE' if the profile has to contain the names of categories
na.rm
Set to 'TRUE' if NAs should be removed