I would like to add a matrix to the DGEList in a similar way assays can be added to a SummarizedExperiment.
I calculated the log transformed cpm values of a DGEList and I would like to store them in the DGEList, so subsetting this object would subset the log transformed cpm values too.
here is my code:
query <- GDCquery(project = "TCGA-BLCA", # project-code for Bladder Cancer data.category = "Transcriptome Profiling", # catogry for RNA-Seq Data data.type = "Gene Expression Quantification", # raw reads, or , aligned data workflow.type = "HTSeq - Counts") # FPKM / HTSeq-Count / etc. GDCdownload(query, # name of the filtered dataset assigned above method = "api", # needs to be set in order to download from the api files.per.chunk = 10, # this should minimise prob. of corruption directory = "GDCdata") # save files to a seperate directory TCGA_BLCA <- GDCprepare(query, summarizedExperiment = TRUE) # Downloads also clinical data TCGA_BLCA_DGEList <- DGEList(TCGA_BLCA) keep <- rowSums(cpm(TCGA_BLCA_DGEList)>0.25) >= 217 TCGA_BLCA_DGEList <- TCGA_BLCA_DGEList[keep, , keep.lib.sizes = FALSE] TCGA_BLCA_DGEList <- calcNormFactors(TCGA_BLCA_DGEList, method = 'upperquartile', p = 0.75) TCGA_BLCA_DGEList = estimateCommonDisp(TCGA_BLCA_DGEList, verbose = TRUE) TCGA_BLCA_DGEList$log2ps_counts <- cpm(TCGA_BLCA_DGEList$pseudo.counts, log = TRUE)
When I now subset my DGEList, log2cpm won´t be subsetted
tumor_tcga <- TCGA_BLCA_DGEList[, TCGA_BLCA_DGEList$samples$shortLetterCode == "TP"] > dim(tumor_tcga$samples)  414 234 > dim(tumor_tcga$log2cpm)  18476 433 > dim(tumor_tcga$counts)  18476 414
I hope you can help me with that.
Thanks and best regards, Aljosch Leusmann