Hello everyone,
I want to use the GDCRNATools to download data and use it later for further analysis.
I have downloaded the RNAseq data using the function gdcRNADownload, then I downloaded the metadata using the gdcParseMetadata, then I removed the duplicates. Later, when I wanted to merge the data, an error occured. Here is my code
`setwd("C:/Users/dell/Desktop/TCGA-UCEC") getwd() library(GDCRNATools) system("gdc-client version", intern = TRUE) project<-"TCGA-UCEC" rnadir <- paste(project, 'RNAseq', sep='/') gdcRNADownload(project.id = 'TCGA-UCEC', data.type = 'RNAseq', write.manifest = FALSE, method = 'gdc-client', ## use gdc-client tool to download data directory = rnadir) MetaMatrix.RNA <- gdcParseMetadata(project.id = 'TCGA-UCEC', data.type = 'RNAseq', write.meta = FALSE) MetaMatrix.RNA <- gdcFilterDuplicate(MetaMatrix.RNA) MetaMatrix.RNA <- gdcFilterSampleType(MetaMatrix.RNA)
rnaCounts <- gdcRNAMerge(metadata = MetaMatrix.RNA, path = rnadir, data.type = 'RNAseq')`
The error that I get:
<h6>######### Merging RNAseq data</h6>This step may take a few minutes
Error in read.table(fl, header = T, stringsAsFactors = F, sep = "\t", : no lines available in the output
Thank you for your replies.
