20 求助...R包RTCGAToolbox 运行Data=getFirehoseData()命令下载Tcga数据出错....

一、各位大侠,小白想用R下载TCGA测序数据进行癌和癌旁基因表达分析,已下载RTCGAToolbox,R3.6.1。

二、下载命令为

Data=getFirehoseData(dataset="THCA",runDate="20160128",clinical=TRUE,RNASeqGene=TRUE,RNAArray=TRUE,Mutation=TRUE)

       出错代码为

Error in file(file, "rt") : cannot open the connection

In addition: Warning messages:
1: In untar(fileLoc, files = fileList, exdir = destdir) :
  ‘tar.exe -xf "./THCA-Mutation.tar.gz" -C "." "gdac.broadinstitute.org_THCA.Mutation_Packager_Calls.Level_3.2016012800.0.0/TCGA-DJ-A1QQ-01.maf.txt" "gdac.broadinstitute.org_THCA.Mutation_Packager_Calls.Level_3.2016012800.0.0/TCGA-DJ-A3VL-01.maf.txt" "gdac.broadinstitute.org_THCA.Mutation_Packager_Calls.Level_3.2016012800.0.0/TCGA-E8-A419-01.maf.txt" "gdac.broadinstitute.org_THCA.Mutation_Packager_Calls.Level_3.2016012800.0.0/TCGA-EM-A4FV-01.maf.txt" "gdac.broadinstitute.org_THCA.Mutation_Packager_Calls.Level_3.2016012800.0.0/TCGA-ET-A2MY-01.maf.txt" "gdac.broadinstitute.org_THCA.Mutation_Packager_Calls.Level_3.2016012800.0.0/TCGA-H2-A3RI-01.maf.txt" "gdac.broadinstitute.org_THCA.Mutation_Packager_Calls.Level_3.2016012800.0.0/TCGA-DJ-A3UM-01.maf.txt" "gdac.broadinstitute.org_THCA.Mutation_Packager_Calls.Level_3.2016012800.0.0/TCGA-BJ-A0Z0-01.maf.txt" "gdac.broadinstitute.org_THCA.Mutation_Packager_Calls.Level_3.2016012800.0.0/TCGA-EL-A3T7-01.maf.txt" "gdac.broadinstitute.org_THCA.Mutati [... truncated]
2: In file(file, "rt") :
  cannot open file 'gdac.broadinstitute.org_THCA.Mutation_Packager_Calls.Level_3.2016012800.0.0/TCGA-DJ-A1QQ-01.maf.txt': No such file or directory

三、尝试重新定义下载路径无效

attachments-2019-09-j8hkFpjP5d888f89d03ab.png

请先 登录 后评论

1 个回答

小张

可以采用TCGAbiolinks下载GDC上的数据

请先 登录 后评论