提起R語言，貌似很艱難

圖文一結合，傻瓜都能填

一、打開R程序

> chooseCRANmirror()

> BiocManager::install("TCGAbiolinks")

更新

> library(TCGAbiolinks)

library(dplyr)

library(DT)

library(SummarizedExperiment)

以宮頸癌CESC為舉例：不同的癌癥類型只需要替換名稱

downlod clinical step：

> cancer_type="TCGA-CESC"

> clinical

> View(clinical)

> save(clinical,file="CESC_clinical.Rdata")

> write.csv(clinical, file="TCGAbiolinks-CESC-clinical.csv")

download RNA-seq step：

> TCGAbiolinks:::getProjectSummary("TCGA-CESC")

> query

? ? ? ? ? ? ? ? ?legacy = FALSE,?

? ? ? ? ? ? ? ? ?experimental.strategy = "RNA-Seq",?

? ? ? ? ? ? ? ? ?data.category = "Transcriptome Profiling",?

? ? ? ? ? ? ? ? ?data.type = "Gene Expression Quantification",?

? ? ? ? ? ? ? ? ?workflow.type = "HTSeq - Counts")

> GDCdownload(query, method = "api", files.per.chunk = 100)

> expdat

> count_matrix=assay(expdat)

> View(count_matrix)

> write.csv(count_matrix,file = "TCGAbiolinks_CESC_counts.csv")

download RNA-seq FPKM step：

> Expr_df

? ? ? ? ? ? ? ? ? ? ?data.category = "Transcriptome Profiling",

? ? ? ? ? ? ? ? ? ? ?data.type = "Gene Expression Quantification",

? ? ? ? ? ? ? ? ? ? ?workflow.type = "HTSeq - FPKM")

> GDCdownload(Expr_df, method = "api", files.per.chunk = 100)

> expdat_2

> Expr_matrix=assay(expdat_2)

> View(Expr_matrix)

> write.csv(Expr_matrix,file = "TCGAbiolinks_CESC_FPKM.csv")

#下載miRNA數據

? query

? ? ? ? ? ? ? ? ? ? data.category = "Transcriptome Profiling",?

? ? ? ? ? ? ? ? ? ? data.type = "miRNA Expression Quantification",?

? ? ? ? ? ? ? ? ? ? workflow.type = "BCGSC miRNA Profiling")

? GDCdownload(query, method = "api", files.per.chunk = 100)

? expdat

? count_matrix=assay(expdat)

? write.csv(count_matrix,file = paste(cancer_type,"miRNA.csv",sep = "-"))

query.mirna

? ? ? ? ? ? ? ? ? ? ? ? experimental.strategy = "miRNA-Seq",

? ? ? ? ? ? ? ? ? ? ? ? data.category = "Transcriptome Profiling",?

? ? ? ? ? ? ? ? ? ? ? ? data.type = "miRNA Expression Quantification")

GDCdownload(query.mirna)

mirna

? ? ? ? ? ? ? ? ? ? ?save = TRUE,?

? ? ? ? ? ? ? ? ? ? ?save.filename = "mirna.rda")

test

write.csv(mirna,"D:\\R語言工作數據\\TCGA\\mirna.csv")

#下載Copy Number Variation數據

? query

? ? ? ? ? ? ? ? ? ? data.category = "Copy Number Variation",?

? ? ? ? ? ? ? ? ? ? data.type = "Copy Number Segment")

? GDCdownload(query, method = "api", files.per.chunk = 50)

? expdat

? count_matrix=assay(expdat)

? write.csv(count_matrix,file = paste(cancer_type,"Copy-Number-Variation.csv",sep = "-"))

#下載甲基化數據

? query.met

? ? ? ? ? ? ? ? ? ? ? ? legacy = TRUE,

? ? ? ? ? ? ? ? ? ? ? ? data.category = "DNA methylation")

? GDCdownload(query.met, method = "api", files.per.chunk = 300)

? expdat

? count_matrix=assay(expdat)

? write.csv(count_matrix,file = paste(cancer_type,"methylation.csv",sep = "-"))

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