git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MineICA@73179 bc3139a8-67e5-0310-9ffc-ced21a209358
Marc Carlson authored on 05/02/2013 22:15:53
| 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,105 @@ |
| 1 |
+\name{annotInGene}
|
|
| 2 |
+\alias{annotInGene}
|
|
| 3 |
+\title{Features annotation of an object of class IcaSet.}
|
|
| 4 |
+\usage{
|
|
| 5 |
+ annotInGene(icaSet, params, annot = TRUE) |
|
| 6 |
+} |
|
| 7 |
+\arguments{
|
|
| 8 |
+ \item{icaSet}{An object of class \code{\link{IcaSet}} to
|
|
| 9 |
+ be annotated, must contain a valid \code{annotation}
|
|
| 10 |
+ attribute.} |
|
| 11 |
+ |
|
| 12 |
+ \item{params}{An object of class
|
|
| 13 |
+ \code{\link{MineICAParams}} containing the parameters of
|
|
| 14 |
+ the analysis.} |
|
| 15 |
+ |
|
| 16 |
+ \item{annot}{TRUE (default) if the IcaSet object must
|
|
| 17 |
+ indeed be annotated} |
|
| 18 |
+} |
|
| 19 |
+\value{
|
|
| 20 |
+ The modified argument \code{icaSet}, with filled
|
|
| 21 |
+ attributes \code{SByGene} and \code{datByGene}.
|
|
| 22 |
+} |
|
| 23 |
+\description{
|
|
| 24 |
+ This function annotates the features of an |
|
| 25 |
+ \code{\link{IcaSet}} object and fills its attributes
|
|
| 26 |
+ \code{SByGene} and \code{datByGene}.
|
|
| 27 |
+} |
|
| 28 |
+\details{
|
|
| 29 |
+ When attribute \code{annotation} of \code{icaSet} is not
|
|
| 30 |
+ specified (of length \code{0}), \code{biomaRt} is used to
|
|
| 31 |
+ annotate the features through function |
|
| 32 |
+ \code{\link{annotFeaturesWithBiomaRt}}.
|
|
| 33 |
+ |
|
| 34 |
+ When specified, attribute \code{annotation} of argument
|
|
| 35 |
+ \code{icaSet} must be an annotation package and will be
|
|
| 36 |
+ used to annotate the \code{featureNames} of
|
|
| 37 |
+ \code{icaSet}. In addition, the attribute \code{typeID}
|
|
| 38 |
+ (a vector) of argument \code{icaSet} must contain a valid
|
|
| 39 |
+ element \code{geneID_annotation} that determines the
|
|
| 40 |
+ object of the package to be used for the annotation, see |
|
| 41 |
+ \code{\link{IcaSet}}.
|
|
| 42 |
+ |
|
| 43 |
+ When argument \code{annot} is TRUE, this function fills
|
|
| 44 |
+ the attributes \code{SByGene} and \code{datByGene} of
|
|
| 45 |
+ \code{icaSet}. When several feature IDs are available for
|
|
| 46 |
+ a same gene ID, the median value of the corresponding |
|
| 47 |
+ features IDs is attributed to the gene (the median of the |
|
| 48 |
+ projection values is used for attribute \code{SByGene},
|
|
| 49 |
+ and the median of the expression values is used for |
|
| 50 |
+ attribute \code{datByGene}).
|
|
| 51 |
+ |
|
| 52 |
+ When attribute \code{chipManu} of the argument
|
|
| 53 |
+ \code{icaSet} is "illumina", the features are first
|
|
| 54 |
+ converted into nuID using the package 'lumi*Mapping' and |
|
| 55 |
+ then annotated into genes. In that case, features can |
|
| 56 |
+ only be annotated in ENTREZID or SYMBOL. It means that |
|
| 57 |
+ \code{typeID(icaSet)['geneID_annotation']} must be either
|
|
| 58 |
+ 'ENTREZID' or 'SYMBOL'. You will need to annotate |
|
| 59 |
+ yourself the IcaSet object if you want to use different |
|
| 60 |
+ IDs. |
|
| 61 |
+} |
|
| 62 |
+\examples{
|
|
| 63 |
+#load data |
|
| 64 |
+data(icaSetCarbayo) |
|
| 65 |
+require(hgu133a.db) |
|
| 66 |
+ |
|
| 67 |
+# run annotation of the features into gene Symbols as specified in 'typeID(icaSetCarbayo)["geneID_annotation"]', |
|
| 68 |
+# using package hgu133a.db as defined in 'annotation(icaSetMainz)' |
|
| 69 |
+icaSetCarbayo <- annotInGene(icaSet=icaSetCarbayo, params=buildMineICAParams()) |
|
| 70 |
+ |
|
| 71 |
+\dontrun{
|
|
| 72 |
+#load data |
|
| 73 |
+library(breastCancerMAINZ) |
|
| 74 |
+data(mainz) |
|
| 75 |
+#run ICA |
|
| 76 |
+resJade <- runICA(X=exprs(mainz), nbComp=5, method = "JADE", maxit=10000) |
|
| 77 |
+ |
|
| 78 |
+#build params |
|
| 79 |
+params <- buildMineICAParams(resPath="mainz/") |
|
| 80 |
+ |
|
| 81 |
+#build a new IcaSet object, omitting annotation of the features (runAnnot=FALSE) |
|
| 82 |
+#but specifying the element "geneID_annotation" of argument 'typeID' |
|
| 83 |
+icaSetMainz <- buildIcaSet(params=params, A=data.frame(resJade$A), S=data.frame(resJade$S), |
|
| 84 |
+ dat=exprs(mainz), pData=pData(mainz), |
|
| 85 |
+ annotation="hgu133a.db", typeID= c(geneID_annotation = "SYMBOL", |
|
| 86 |
+ geneID_biomart = "hgnc_symbol", featureID_biomart = "affy_hg_u133a"), |
|
| 87 |
+ chipManu = "affymetrix", runAnnot=FALSE, |
|
| 88 |
+ mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")) |
|
| 89 |
+ |
|
| 90 |
+#Attributes SByGene is empty and attribute datByGene refers to assayData |
|
| 91 |
+SByGene(icaSetMainz) |
|
| 92 |
+head(datByGene(icaSetMainz)) |
|
| 93 |
+ |
|
| 94 |
+# run annotation of the features into gene Symbols as specified in 'typeID(icaSetMainz)["geneID_annotation"]', |
|
| 95 |
+# using package hgu133a.db as defined in 'annotation(icaSetMainz)' |
|
| 96 |
+icaSetMainz <- annotInGene(icaSet=icaSetMainz, params=params) |
|
| 97 |
+} |
|
| 98 |
+} |
|
| 99 |
+\author{
|
|
| 100 |
+ Anne Biton |
|
| 101 |
+} |
|
| 102 |
+\seealso{
|
|
| 103 |
+ \code{\link{annotFeaturesComp}}
|
|
| 104 |
+} |
|
| 105 |
+ |