## ----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) ## ---- eval = TRUE, echo = FALSE------------------------------------------ datatable(TCGAbiolinks:::getGDCprojects(), filter = 'top', options = list(scrollX = TRUE, keys = TRUE, pageLength = 10), rownames = FALSE, caption = "List of projects") ## ---- eval = TRUE, echo = FALSE------------------------------------------ datatable(TCGAbiolinks:::getBarcodeDefinition(), filter = 'top', options = list(scrollX = TRUE, keys = TRUE, pageLength = 10), rownames = FALSE, caption = "List sample types") ## ------------------------------------------------------------------------ datatable(readr::read_csv("https://docs.google.com/spreadsheets/d/1f98kFdj9mxVDc1dv4xTZdx8iWgUiDYO-qiFJINvmTZs/export?format=csv&gid=2046985454"), filter = 'top', options = list(scrollX = TRUE, keys = TRUE, pageLength = 40), rownames = FALSE) ## ------------------------------------------------------------------------ datatable(readr::read_csv("https://docs.google.com/spreadsheets/d/1f98kFdj9mxVDc1dv4xTZdx8iWgUiDYO-qiFJINvmTZs/export?format=csv&gid=1817673686"), filter = 'top', options = list(scrollX = TRUE, keys = TRUE, pageLength = 40), rownames = FALSE) ## ----message=FALSE, warning=FALSE---------------------------------------- query <- GDCquery(project = c("TCGA-GBM", "TCGA-LGG"), data.category = "DNA Methylation", legacy = FALSE, platform = c("Illumina Human Methylation 450"), sample.type = "Recurrent Solid Tumor" ) datatable(getResults(query), filter = 'top', options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), rownames = FALSE) ## ----message=FALSE, warning=FALSE---------------------------------------- query.met <- GDCquery(project = "TCGA-COAD", data.category = "DNA Methylation", legacy = FALSE, platform = c("Illumina Human Methylation 450")) query.exp <- GDCquery(project = "TCGA-COAD", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", workflow.type = "HTSeq - FPKM-UQ") # Get all patients that have DNA methylation and gene expression. common.patients <- intersect(substr(getResults(query.met, cols = "cases"), 1, 12), substr(getResults(query.exp, cols = "cases"), 1, 12)) # Only seelct the first 5 patients query.met <- GDCquery(project = "TCGA-COAD", data.category = "DNA Methylation", legacy = FALSE, platform = c("Illumina Human Methylation 450"), barcode = common.patients[1:5]) query.exp <- GDCquery(project = "TCGA-COAD", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", workflow.type = "HTSeq - FPKM-UQ", barcode = common.patients[1:5]) datatable(getResults(query.met, cols = c("data_type","cases")), filter = 'top', options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), rownames = FALSE) datatable(getResults(query.exp, cols = c("data_type","cases")), filter = 'top', options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), rownames = FALSE) ## ----message=FALSE, warning=FALSE---------------------------------------- query <- GDCquery(project = c("TCGA-BRCA"), data.category = "Raw Sequencing Data", sample.type = "Primary solid Tumor") # Only first 100 to make render faster datatable(getResults(query, rows = 1:100,cols = c("file_name","cases")), filter = 'top', options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), rownames = FALSE) ## ----message=FALSE, warning=FALSE---------------------------------------- query <- GDCquery(project = c("TCGA-GBM","TCGA-LGG"), legacy = TRUE, data.category = "DNA methylation", platform = c("Illumina Human Methylation 450", "Illumina Human Methylation 27")) datatable(getResults(query, rows = 1:100), filter = 'top', options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), rownames = FALSE) ## ----message=FALSE, warning=FALSE---------------------------------------- # Gene expression aligned against hg19. query.exp.hg19 <- GDCquery(project = "TCGA-GBM", data.category = "Gene expression", data.type = "Gene expression quantification", platform = "Illumina HiSeq", file.type = "normalized_results", experimental.strategy = "RNA-Seq", barcode = c("TCGA-14-0736-02A-01R-2005-01", "TCGA-06-0211-02A-02R-2005-01"), legacy = TRUE) datatable(getResults(query.exp.hg19), filter = 'top', options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), rownames = FALSE)