## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) knitr::opts_knit$set(progress = FALSE) ## ----message=FALSE, warning=FALSE, include=FALSE------------------------------ library(TCGAbiolinks) library(SummarizedExperiment) library(dplyr) library(DT) ## ----results = 'hide', message=FALSE, warning=FALSE, eval=FALSE--------------- # # Gene expression aligned against hg38 # query <- GDCquery( # project = "TCGA-GBM", # data.category = "Transcriptome Profiling", # data.type = "Gene Expression Quantification", # workflow.type = "STAR - Counts", # barcode = c("TCGA-14-0736-02A-01R-2005-01", "TCGA-06-0211-02A-02R-2005-01") # ) # GDCdownload(query = query) # data <- GDCprepare(query = query) ## ----message=FALSE, warning=FALSE, include=FALSE------------------------------ data <- gbm.exp.harmonized ## ----message=FALSE, warning=FALSE--------------------------------------------- datatable( as.data.frame(colData(data)), options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), rownames = FALSE ) datatable( assay(data)[1:20,], options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), rownames = TRUE ) rowRanges(data) ## ----eval = FALSE------------------------------------------------------------- # query <- GDCquery( # project = "TCGA-ACC", # data.category = "Copy Number Variation", # data.type = "Copy Number Segment", # barcode = c( "TCGA-OR-A5KU-01A-11D-A29H-01", "TCGA-OR-A5JK-01A-11D-A29H-01") # ) # GDCdownload(query) # data <- GDCprepare(query) ## ----eval = FALSE------------------------------------------------------------- # query <- GDCquery( # project = "TCGA-ACC", # data.category = "Copy Number Variation", # data.type = "Gene Level Copy Number", # access = "open" # ) # GDCdownload(query) # data <- GDCprepare(query) ## ----eval = FALSE------------------------------------------------------------- # query <- GDCquery( # project = "TCGA-ACC", # data.category = "Copy Number Variation", # data.type = "Allele-specific Copy Number Segment", # access = "open" # ) # GDCdownload(query) # data <- GDCprepare(query) ## ----eval = FALSE------------------------------------------------------------- # query <- GDCquery( # project = "TCGA-ACC", # data.category = "Copy Number Variation", # data.type = "Masked Copy Number Segment", # access = "open" # ) # GDCdownload(query) # data <- GDCprepare(query) ## ----eval = FALSE------------------------------------------------------------- # # mRNA pipeline: https://gdc-docs.nci.nih.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/ # query.exp.hg38 <- GDCquery( # project = "TCGA-GBM", # data.category = "Transcriptome Profiling", # data.type = "Gene Expression Quantification", # workflow.type = "STAR - Counts", # barcode = c("TCGA-14-0736-02A-01R-2005-01", "TCGA-06-0211-02A-02R-2005-01") # ) # GDCdownload(query.exp.hg38) # expdat <- GDCprepare( # query = query.exp.hg38, # save = TRUE, # save.filename = "exp.rda" # ) ## ----eval = FALSE------------------------------------------------------------- # library(TCGAbiolinks) # query.mirna <- GDCquery( # project = "TARGET-AML", # experimental.strategy = "miRNA-Seq", # data.category = "Transcriptome Profiling", # barcode = c("TARGET-20-PATDNN","TARGET-20-PAPUNR"), # data.type = "miRNA Expression Quantification" # ) # GDCdownload(query.mirna) # mirna <- GDCprepare( # query = query.mirna, # save = TRUE, # save.filename = "mirna.rda" # ) # ## ----eval = FALSE------------------------------------------------------------- # # query.isoform <- GDCquery( # project = "TARGET-AML", # experimental.strategy = "miRNA-Seq", # data.category = "Transcriptome Profiling", # barcode = c("TARGET-20-PATDNN","TARGET-20-PAPUNR"), # data.type = "Isoform Expression Quantification" # ) # GDCdownload(query.isoform) # # isoform <- GDCprepare( # query = query.isoform, # save = TRUE, # save.filename = "mirna-isoform.rda" # ) ## ----eval = FALSE------------------------------------------------------------- # query_met.hg38 <- GDCquery( # project = "TCGA-BRCA", # data.category = "DNA Methylation", # data.type = "Methylation Beta Value", # platform = "Illumina Human Methylation 27", # barcode = c("TCGA-B6-A0IM") # ) # GDCdownload(query_met.hg38) # data.hg38 <- GDCprepare(query_met.hg38) # # query_met.hg38 <- GDCquery( # project= "TCGA-LGG", # data.category = "DNA Methylation", # data.type = "Methylation Beta Value", # platform = "Illumina Human Methylation 450", # barcode = c("TCGA-HT-8111-01A-11D-2399-05","TCGA-HT-A5R5-01A-11D-A28N-05") # ) # GDCdownload(query_met.hg38) # data.hg38 <- GDCprepare(query_met.hg38) # # # query_met.hg38 <- GDCquery( # project= "HCMI-CMDC", # data.category = "DNA Methylation", # data.type = "Methylation Beta Value", # platform = "Illumina Methylation Epic", # barcode = c("HCM-BROD-0045") # ) # GDCdownload(query_met.hg38) # data.hg38 <- GDCprepare(query_met.hg38) ## ----eval = FALSE------------------------------------------------------------- # query <- GDCquery( # project = "TCGA-BRCA", # data.category = "DNA Methylation", # data.type = "Masked Intensities", # platform = "Illumina Human Methylation 27" # ) # GDCdownload(query, files.per.chunk=10) # betas <- GDCprepare(query) # # query <- GDCquery( # project = "HCMI-CMDC", # data.category = "DNA Methylation", # data.type = "Masked Intensities", # platform = "Illumina Methylation Epic" # ) # GDCdownload(query, files.per.chunk = 10) # betas <- GDCprepare(query) # # # query <- GDCquery( # project = "CPTAC-3", # data.category = "DNA Methylation", # data.type = "Masked Intensities", # platform = "Illumina Methylation Epic" # ) # GDCdownload(query, files.per.chunk=10) # betas <- GDCprepare(query) # # query <- GDCquery( # project = "TCGA-BRCA", # data.category = "DNA Methylation", # data.type = "Masked Intensities", # platform = "Illumina Methylation Epic" # ) # GDCdownload(query, files.per.chunk = 10) # betas <- GDCprepare(query) # # ## ----eval = FALSE------------------------------------------------------------- # query.rppa <- GDCquery( # project = "TCGA-ESCA", # data.category = "Proteome Profiling", # data.type = "Protein Expression Quantification" # ) # GDCdownload(query.rppa) # rppa <- GDCprepare(query.rppa) ## ----eval = FALSE------------------------------------------------------------- # # query <- GDCquery( # project = "TCGA-COAD", # data.category = "Clinical", # data.type = "Clinical Supplement", # data.format = "BCR XML", # barcode = "TCGA-A6-5664" # ) # GDCdownload(query) # drug <- GDCprepare_clinic(query,"drug") # # query <- GDCquery( # project = "TCGA-COAD", # data.category = "Clinical", # data.type = "Clinical Supplement", # data.format = "BCR OMF XML", # barcode = "TCGA-AD-6964" # ) # GDCdownload(query) # # # query <- GDCquery( # project = "TCGA-ACC", # data.category = "Clinical", # data.type = "Clinical Supplement", # data.format = "BCR Biotab" # ) # GDCdownload(query) # clinical.BCRtab.all <- GDCprepare(query) # names(clinical.BCRtab.all) # # query <- GDCquery( # project = "TCGA-ACC", # data.category = "Clinical", # data.type = "Clinical Supplement", # data.format = "BCR Biotab", # file.type = "radiation" # ) # GDCdownload(query) # clinical.BCRtab.radiation <- GDCprepare(query) ## ----eval = FALSE------------------------------------------------------------- # query <- GDCquery( # project = "TCGA-HNSC", # data.category = "Simple Nucleotide Variation", # data.type = "Masked Somatic Mutation", # access = "open" # ) # GDCdownload(query) # maf <- GDCprepare(query) ## ----eval = FALSE------------------------------------------------------------- # query.sc.analysis <- GDCquery( # project = "CPTAC-3", # data.category = "Transcriptome Profiling", # access = "open", # data.type = "Single Cell Analysis", # data.format = "TSV" # ) # GDCdownload(query.sc.analysis) # Single.Cell.Analysis.list <- GDCprepare(query.sc.analysis) ## ----eval = FALSE,include=F--------------------------------------------------- # query.hdF5 <- GDCquery( # project = "CPTAC-3", # data.category = "Transcriptome Profiling", # access = "open", # data.type = "Single Cell Analysis", # barcode = c("CPT0167860015","CPT0206880004"), # data.format = "HDF5" # ) # GDCdownload(query.hdF5) # df.HDF5 <- GDCprepare(query.hdF5) ## ----eval = FALSE------------------------------------------------------------- # query.raw.counts <- GDCquery( # project = "CPTAC-3", # data.category = "Transcriptome Profiling", # access = "open", # data.type = "Gene Expression Quantification", # barcode = c("CPT0167860015","CPT0206880004"), # workflow.type = "CellRanger - 10x Raw Counts" # ) # GDCdownload(query.raw.counts) # raw.counts.list <- GDCprepare(query.raw.counts) ## ----eval = FALSE------------------------------------------------------------- # query.filtered.counts <- GDCquery( # project = "CPTAC-3", # data.category = "Transcriptome Profiling", # access = "open", # data.type = "Gene Expression Quantification", # barcode = c("CPT0167860015","CPT0206880004"), # workflow.type = "CellRanger - 10x Filtered Counts" # ) # GDCdownload(query.filtered.counts) # filtered.counts.list <- GDCprepare(query.filtered.counts) ## ----eval = FALSE------------------------------------------------------------- # query.sc.dea <- GDCquery( # project = "CPTAC-3", # data.category = "Transcriptome Profiling", # access = "open", # data.type = "Differential Gene Expression", # barcode = c("CPT0167860015","CPT0206880004"), # workflow.type = "Seurat - 10x Chromium" # ) # GDCdownload(query.sc.dea) # sc.dea.list <- GDCprepare(query.sc.dea)