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TCGAbiolinks
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GDCprepare() returns Error in function (classes, fdef, mtable) Methylation percentage #557

Open CamilleWangermez opened 1 year ago

CamilleWangermez commented 1 year ago

Hello, I have downloaded TCGA data of methylation percentage for all the tumor types (COAD, READ, STAD, BRCA, GBM, BLCA, UCEC, LUSC, LUAD). After the download I have an error when I run GDCprepare (see below). I tried to investigate the error and it lead me to the Issues #478 and #198.
But I didn't understand how I can apply the discussions on my data. What could I do?

Thanks in advance, Camille

setwd("/data/gepi/Data/TCGA/Bisulfite_seq")

library(TCGAbiolinks)

query_bis_LUAD <- GDCquery(project = "TCGA-LUAD",
                           data.category = "DNA methylation",
                           legacy = TRUE, 
                           data.type = "Methylation percentage")
#> --------------------------------------
#> o GDCquery: Searching in GDC database
#> --------------------------------------
#> Genome of reference: hg19
#> --------------------------------------------
#> oo Accessing GDC. This might take a while...
#> --------------------------------------------
#> ooo Project: TCGA-LUAD
#> --------------------
#> oo Filtering results
#> --------------------
#> ooo By data.type
#> ----------------
#> oo Checking data
#> ----------------
#> ooo Checking if there are duplicated cases
#> ooo Checking if there are results for the query
#> -------------------
#> o Preparing output
#> -------------------

GDCdownload(query_bis_LUAD, directory = "TCGA_LUAD_bis", method = "client")
#> Downloading data for project TCGA-LUAD
#> Of the 6 files for download 6 already exist.
#> All samples have been already downloaded

GDCprepare(query_bis_LUAD, directory = "TCGA_LUAD_bis")
#> Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'metadata<-' for signature '"function"'

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