BiocManager::install("ExperimentHub")
library(ExperimentHub)
eh = ExperimentHub()
query(eh, "GSE62944")
tcga_data <- eh[["EH1"]]
lgg_data <- tcga_data[, which(phenoData(tcga_data)$CancerType=="LGG")]
mut_idx <- which(phenoData(lgg_data)$idh1_mutation_found=="YES")
mut_data <- exprs(lgg_data)[, mut_idx]
wt_idx <- which(phenoData(lgg_data)$idh1_mutation_found=="NO")
wt_data <- exprs(lgg_data)[, wt_idx]
countData <- cbind(mut_data, wt_data)
samples= c(colnames(mut_data), colnames(wt_data))
group =c(rep("mut",length(mut_idx)), rep("wt", length(wt_idx)))
coldata <- cbind(samples, group)
colnames(coldata) <- c("sampleName", "Group")
coldata[,"Group"] <- factor(coldata[,"Group"], c("wt","mut"))
library(pcaExplorer)
pcaExplorer(countmatrix = countData, coldata = coldata)