I'm looking PAM50 molecular Subtypes of TCGA Breast RNA-Seq data. I'm using the following code. But I'm having an error with TCGAquery function. I have used similar code long back and it worked but now it is not working with TCGAquery function.
cancer <- "BRCA"
PlatformCancer <- "IlluminaHiSeq_RNASeqV2"
dataType <- "rsem.genes.results"
pathCancer <- "TCGAData/miRNA"
datQuery <- TCGAquery(tumor = cancer, platform = PlatformCancer, level = "3")
Error in TCGAquery(tumor = cancer, platform = PlatformCancer, level = "3") : could not find function "TCGAquery"
lsSample <- TCGAquery_samplesfilter(query = datQuery)
# get subtype information
dataSubt <- TCGAquery_subtype(tumor = cancer)
lumA <- dataSubt[which(dataSubt$PAM50.mRNA == "Luminal A"),1]
allSamples <- lsSample$IlluminaHiSeq_RNASeqV2 #1218 total samples
Any help please !!