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
Details
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.
Value
An object of class GOProfile (one or more data frames in a list named by the ontologies)
Author(s)
Alex Sanchez
References
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
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)
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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(goProfiles)
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, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
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 objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: GO.db
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/goProfiles/basicProfile.Rd_%03d_medium.png", width=480, height=480)
> ### Name: basicProfile
> ### Title: Builds basic functional profile
> ### Aliases: basicProfile
> ### Keywords: htest
>
> ### ** Examples
>
> data(CD4Ids)
> CD4.MF.Profiles <-basicProfile(genelist=CD4LLids, onto='MF', level=2, orgPackage="org.Hs.eg.db")
> print(CD4.MF.Profiles)
$MF
Description GOID Frequency
14 D-alanyl carrier activity GO:0036370 0
12 antioxidant activity GO:0016209 3
9 binding GO:0005488 109
4 catalytic activity GO:0003824 48
15 chemoattractant activity GO:0042056 2
17 chemorepellent activity GO:0045499 0
1 electron carrier activity GO:0009055 1
13 metallochaperone activity GO:0016530 0
19 molecular function regulator GO:0098772 10
18 molecular transducer activity GO:0060089 13
11 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 11
7 structural molecule activity GO:0005198 7
2 transcription factor activity, protein binding GO:0000988 4
16 translation regulator activity GO:0045182 2
8 transporter activity GO:0005215 15
>
>
>
>
>
> dev.off()
null device
1
>