Ways to manipulate Expression Sets for HW3

expressionSetManipulation.R

# Some useful ways to manipulate expressionSets
# Please cite me if you use this code

library(Hiiragi2013)

# load data
data(x)

# Show sample Information
pData(phenoData(x))

# Show names of columns in sample Information
varLabels(x)

# We want to subset based on genotype
x$genotype

#grab indices where genotype == "WT"
WT <- grep("WT", x$genotype)
WT

#This also works
WTL <- x$genotype == "WT"
WTL

#grab only the WT data
#these are identical
WTdata <- x[,WTL]
WTdata2 <- x[,WT]

#extract the expression matrix
exp_matrix <- Biobase::exprs(x[,WTL])

#recode the data as classes
E325classes <- ifelse(WTdata$sampleGroup =="E3.25", 1, 0)
#show that we coded them correctly
data.frame(WTdata$sampleGroup, E325classes)

#add these labels back to the expressionSet
WTdata$E325classes <- E325classes

#Show we added them back
pData(phenoData(WTdata))

#Sample Random columns
numSamples <- ncol(WTdata)
randomSample <- sample.int(n=numSamples, size=10, replace = FALSE)

#confirm that we sampled correctly
randomSample

#make a new sampled set from the WTdata
sampledWT <- WTdata[,randomSample]
sampleNames(sampledWT)

#Confirm that the classes are correct
sampledWT$E325classes