# #设置,包括= FALSE ------------------------------------------------ knitr: opts_chunk设置(echo = TRUE) knitr:美元:opts_knit设置(进步= FALSE) # #——美元消息= FALSE,警告= FALSE,包括= FALSE ------------------------- 图书馆(TCGAbiolinks)图书馆(SummarizedExperiment)图书馆(dplyr)图书馆(DT ) ## ---- eval = TRUE,回声= FALSE ------------------------------------------ datatable (TCGAbiolinks::: getGDCprojects(),过滤器=“高级”,选择=列表(scrollX = TRUE,键= TRUE,pageLength = 10)， rownames = FALSE，标题= "项目列表")## ---- eval = TRUE, echo = FALSE------------------------------------------ datatable(TCGAbiolinks:::getBarcodeDefinition()， filter = 'top'， options = List (scrollX = TRUE, keys = TRUE, pageLength = 10)， rownames = FALSE，标题= "样本类型列表 ") ## ------------------------------------------------------------------------ 数据表(readr:: read_csv(“https://docs.google.com/spreadsheets/d/1f98kFdj9mxVDc1dv4xTZdx8iWgUiDYO-qiFJINvmTZs/export?format=csv&gid=2046985454”),过滤器=“顶级”,选项=列表(scrollX = TRUE,键= TRUE, pageLength = 40),rownames = FALSE ) ## ------------------------------------------------------------------------ 数据表(readr:: read_csv(“https://docs.google.com/spreadsheets/d/1f98kFdj9mxVDc1dv4xTZdx8iWgUiDYO-qiFJINvmTZs/export?format=csv&gid=1817673686”),过滤器=“顶级”,选项=列表(scrollX = TRUE,键= TRUE, pageLength = 40), rownames = FALSE) # # = FALSE,消息,警告= FALSE ---------------------------------------- 查询< - GDCquery(项目= c(“TCGA-GBM”、“TCGA-LGG”),数据。类别=“DNA甲基化”，遗产=假，平台= c(“Illumina人类甲基化450”)，样本。type = "复发性实体瘤”)数据表(getResults(查询),过滤器=“高级”,选择=列表(scrollX = TRUE,键= TRUE, pageLength = 5), rownames = FALSE) # # = FALSE,消息,警告= FALSE ---------------------------------------- 查询。<- GDCquery(project = "TCGA-COAD"， data. GDCquery <- GDCquery(project = "TCGA-COAD"， data。category = "DNA甲基化"，legacy = FALSE, platform = c("Illumina Human Methylation 450"))查询。exp <- GDCquery(项目= "TCGA-COAD"，数据。category =“转录组分析”，数据。type = "基因表达量化"，工作流。type = "HTSeq - FPKM-UQ") #获取所有DNA甲基化和基因表达的患者。常见的。- 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)