basicProfile: Builds basic functional profile
In goProfiles: goProfiles: an R package for the statistical analysis of functional profiles

Description Usage Arguments Details Value Author(s) References See Also Examples

Compute basic functional profile for a given list of genes/GO identifiers, a given ontology at a given level of the GO

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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)

`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

The function admits three types of entries: Entrez ('Entrez'), Bioconductor probe set names ('BioCprobes') or a special type of data frames ('GOTermsFrames'). If the identifier type are 'BioCprobes' then an annotation package name must be provided too.

An object of class GOProfile (one or more data frames in a list named by the ontologies)

Alex Sanchez

Sanchez-Pla, A., Salicru, M. and Ocana, J. Statistical methods for the analysis of high-throughput data based on functional profiles derived from the gene ontology. Journal of Statistical Planning and Inference, Volume 137, Issue 12, Pages 3975-3989, 2007

expandedProfile

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data(CD4Ids)
CD4.MF.Profiles <-basicProfile(genelist=CD4LLids, onto='MF', level=2, orgPackage="org.Hs.eg.db")
print(CD4.MF.Profiles)

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: GO.db


$MF
                                          Description       GOID Frequency
15                          D-alanyl carrier activity GO:0036370         0
13                               antioxidant activity GO:0016209         3
9                                             binding GO:0005488       110
4                                  catalytic activity GO:0003824        50
16                           chemoattractant activity GO:0042056         2
18                            chemorepellent activity GO:0045499         0
1                           electron carrier activity GO:0009055         1
14                          metallochaperone activity GO:0016530         0
20                       molecular function regulator GO:0098772        15
19                      molecular transducer activity GO:0060089        14
12                                 morphogen activity GO:0016015         0
3  nucleic acid binding transcription factor activity GO:0001071         7
6                         nutrient reservoir activity GO:0045735         0
10                                        protein tag GO:0031386         0
5                          signal transducer activity GO:0004871        13
7                        structural molecule activity GO:0005198         7
11                                     toxin activity GO:0090729         0
2      transcription factor activity, protein binding GO:0000988         4
17                     translation regulator activity GO:0045182         2
8                                transporter activity GO:0005215        15

Warning message:
system call failed: Cannot allocate memory