processing data from local fold using TCGAbiolinks

Question

[283430749]

Dear everyone How do I use GDCprepare_clinic() to prepare data that already downloaded in local folder from the GDC cart? thank alot

[noorpratap.singh]

In the following command replace "GDCdata" with the local folder name. GDCprepare_clinic(query, directory = "GDCdata")

[283430749]

Thank you for reply. I tried but it did not work. the directory was OK, should i change the query argument, for it was still the object returned from GDCquery function.

query <- GDCquery(project = tcga_project, data.category = data_category, data.type = data_type, file.type = file_type, legacy = legacy) clinical <- GDCprepare_clinic(query, clinical.info = "patient",directory = "C:/Users/admin/Desktop/gdc_download_20190413_045634.449501") Error in GDCprepare_clinic(query, clinical.info = "patient", directory = "C:/Users/admin/Desktop/gdc_download_20190413_045634.449501") : I couldn't find all the files from the query.Please check directory parameter right

Answer 1

[283430749]

query <- GDCquery(project = tcga_project, data.category = data_category, data.type = data_type, file.type = file_type, legacy = legacy) clinical <- GDCprepare_clinic(query, clinical.info = "patient",directory = "C:/Users/admin/Desktop/gdc_download_20190413_045634.449501") Error in GDCprepare_clinic(query, clinical.info = "patient", directory = "C:/Users/admin/Desktop/gdc_download_20190413_045634.449501") : I couldn't find all the files from the query.Please check directory parameter right

[noorpratap.singh]

The folder you mention, does it contain all the files listed by query. To see the total files by query use the following:

nrow(query$results[[1]])

Compare with the total downloaded files in your folder.

Further could you send me the exact query you used as it would be then easier to troubleshoot. Also send the output of the following command

getwd()