TCGAbiolinks数据下载miRNA失败

TCGAbiolinks数据下载miRNA失败

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新建一个文件夹00_data_read_in_one_file用于存放所有的文件

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设置工作目录到00_data_read_in_one_file文件夹内，查看文件数目

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在使用gdcRNAtools 时会有一个这样的命令，就是

####### Filter duplicated samples in miRNAs metadata #######

metaMatrix_filter_dupli <- gdcFilterDuplicate(metaMatrix.MIR)

是因为下面的情况存在

zai

TCGAbiolinks下载之后，用GDCRNAtools读取即可

query_miRNA = GDCquery(project = "TCGA-CESC",  experimental.strategy = "miRNA-Seq", data.category = "Transcriptome Profiling", data.type = "Isoform Expression Quantification", workflow.type = "BCGSC miRNA Profiling")

GDCdownload(query_miRNA)

####### Parse miRNAs metadata #######
metaMatrix.MIR <- gdcParseMetadata(project.id = 'TCGA-CESC',
                                   data.type  = 'miRNAs', 
                                   write.meta = FALSE)

####### Filter duplicated samples in miRNAs metadata #######
metaMatrix.MIR <- gdcFilterDuplicate(metaMatrix.MIR)

####### Filter non-Primary Tumor and non-Solid Tissue Normal samples in miRNAs metadata #######
metaMatrix.MIR <- gdcFilterSampleType(metaMatrix.MIR)
save(metaMatrix.MIR,file = "metaMatrix.rda")

####### Merge miRNAs data #######
mirCounts <- gdcRNAMerge(metadata  = metaMatrix.MIR,
                         path      = "F:/医学方/ceRNA/ceRNA/miRNA", # the folder in which the data stored
                         organized = FALSE, # if the data are in separate folders
                         data.type = 'miRNAs')

gdcRNAtools 下载metadata总是报错,和网络有很大关系

####### Parse RNAseq metadata #######

metaMatrix.RNA <- gdcParseMetadata(project.id = 'TCGA-BRCA',
                                   data.type  = 'RNAseq', 
                                   write.meta = FALSE)

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