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rli012 / GDCRNATools

GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA and mRNA data in GDC
Apache License 2.0
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Can not parse metadata by providing the metadata file. #2

Open thy-chan opened 6 years ago

thy-chan commented 6 years ago

I'm trying to use 'gdcParseMetadata()' to parse metadata by providing the metadata file, but find that the format of the metadata file in GDC has been change recently. So, I want to know how long the GDCRNATools can be updated. Thanks!

` ##############################################################################

Error in vapply(seq_len(nSam), function(i) metadata[[i]]$cases[[1]]$samples[[1]]$submitter_id, : 值的长度必需为1， 但FUN(X[[1]])结果的长度却是0 Calls: source ... withVisible -> eval -> eval -> gdcParseMetadata -> vapply 停止执行 `

Jialab-UCR commented 6 years ago

@thy-chan Hi, could you please tell me the project you are trying to parse? Thanks

thy-chan commented 6 years ago

RNA-Seq files in TCGA-BRCA. The format of the metadata file has changed so that the GDCRNATools can't parse it. image

Jialab-UCR commented 6 years ago

@thy-chan Thank you so much for the reminder. I have just checked the JSON file in GDC and they do have changed the format. There's very little information in the file now, so I recommend that you can parse metadata use the automatic mode (eg., meta <- gdcParseMeta(project.id='TCGA-BRCA', data.type='RNAseq'), and then select the sample you'd like to use. Thanks

thy-chan commented 6 years ago

Yes, the information in the GDC's JSON file is reduced. I think the GDC extracts other information separately and puts it in other files, such as the Biospecimen and Sample sheet in the screenshot. Thanks

brcangs commented 6 years ago

Parsing the metadata using the automatic mode for the TCGA-BRCA project does unfortunately not seem to work either:

> metaMatrix <- gdcParseMetadata(project.id='TCGA-BRCA', data.type='RNAseq') Error in vapply(seq_len(nSam), function(i) null2naFun(metadata[[i]]$cases[[1]]$demographic$gender), : values must be type 'character', but FUN(X[[297]]) result is type 'logical'

ChengYunazhi commented 6 years ago

I got a same error when parsing TCGA-COAD metadata, here it is: qq 20180823170957

the command used: qq 20180823171348

yinlisssss commented 6 years ago

HI, is this because of my internet problem? or? thank you very much

metaMatrix.MIR <- gdcParseMetadata(project.id = "TCGA-LUSC",

  • data.type = "miRNAs") Error in file(con, "r") : cannot open the connection In addition: Warning message: In file(con, "r") : InternetOpenUrl failed: '操作超时'
CavinChan commented 6 years ago

I got an error when automatic download RNAseq data, here it is: image the command used: image an error when Merge RNAseq data: image thank you very much