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### R code for Stats Computing 1 lecture on Bioconductor ###
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### Date: 4/4/2013						   ###
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### Installing bioconductor
source("http://bioconductor.org/biocLite.R")
biocLite()
biocLite("Biobase")
library(Biobase)

### Help for bioconductor packages(i.e. vignettes)
help(Biobase)
library(help=”Biobase”)
browseVingettes(package=”Biobase”)


### Example of data and meta-data in bioconductor
data(sample.ExpressionSet)
sample.ExpressionSet
class(sample.ExpressionSet)


### S3 class object
x<-rnorm(100); y<-rnorm(100)
fit<-lm(y~x)
class(fit)
#slotNames(fit)
names(fit); fit$coefficients
class(sample.ExpressionSet)
names(sample.ExpressionSet)

###Working with an S4 class object in R
slotNames(sample.ExpressionSet)
sample.ExpressionSet@experimentData

###Looking at features of the data
abstract(sample.ExpressionSet)
#Variable names of the data
varMetadata(sample.ExpressionSet) 
#Names of the genes	
featureNames(sample.ExpressionSet) 
#Expression values for the genes
exprs(sample.ExpressionSet)

### Visulaizing the data
dim(sample.ExpressionSet)
plot(density(exprs(sample.ExpressionSet)[,1]), xlim=c(0,6000), ylim=c(0, 0.006), main="Sample densities")
for (i in 2:25){
lines(density(exprs(sample.ExpressionSet)[,i]), col=i) }

### Subsetting the data
sample.ExpressionSet$sex 
subESet<-sample.ExpressionSet[1:10,] 
exprs(sample.ExpressionSet)[1:10,]
exprs(subESet)


### Subsetting on gender
f.ids<-which(sample.ExpressionSet$sex=="Female")
femalesESet<-sample.ExpressionSet[,f.ids]

### Subsetting on AFFX genes using the grep command
AFFX.ids<-grep("AFFX", featureNames(sample.ExpressionSet))
AFFX.ESet<-sample.ExpressionSet[AFFX.ids,]