TCGAbiolinks MSI data
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Entering edit mode
10 months ago
Elizabeth ▴ 10

Hi! I am trying to use this code to access Microsatellita data:

query <- GDCquery(project = "TCGA-COAD", 
                  data.category = "Other",
                  legacy = TRUE,
                  access = "open",
                  data.type = "Auxiliary test",
                  barcode = c("TCGA-AD-A5EJ","TCGA-DM-A0X9")) 

from TCGAbiolinks help documents, but I have this error message: "Error in checkDataCategoriesInput(project, data.category, legacy) : Please set a valid data.category argument from the column data_category above. We could not validade the data.category for project TCGA-COAD"

What data.category should I use? (because data.category = "Other" doesn't exist)

Thanks!

msi • 449 views
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Entering edit mode

Please check that TCGAbiolinks does not have Other in the data.category option. Please check the options available for this function simply running-

?GDCquery()

And do not provide parameters blindly.

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