Difficulty in downloading TCGA data - r

Question

I am trying to download the TCGA data but I am getting this error:
Error in summarizeMaf(maf = maf, anno = clinicalData, chatty =
verbose): Tumor_Sample_Barcode column not found in provided clinical
data. Rename column containing sample names to Tumor_Sample_Barcode if
necessary.
This is my code:
library("TCGAbiolinks")
library("tidyverse")
library(maftools)
query <- GDCquery( project = "TCGA-LIHC",
data.category = "Clinical",
file.type = "xml",
legacy = FALSE)
GDCdownload(query,directory = ".")
clinical <- GDCprepare_clinic(query, clinical.info = "patient",directory = ".")
#getting the survival time of event data
survival_data <- as_tibble(clinical[,c("days_to_last_followup","days_to_death","vital_status","bcr_patient_barcode","patient_id")])
survival_data <- filter(survival_data,!is.na(days_to_last_followup)|!is.na(days_to_death)) #not both NA
survival_data <- filter(survival_data,!is.na(days_to_last_followup)|days_to_last_followup>0 &is.na(days_to_death)|days_to_death > 0 ) #ensuring positive values
survival_data <- survival_data[!duplicated(survival_data$patient_id),] #ensuring no duplicates
dim(survival_data) #should be 371
maf <- GDCquery_Maf("LIHC", pipelines = "muse")
#maf <- GDCquery_Maf("LIHC", pipelines = "somaticsniper")
#clin <- GDCquery_clinic("TCGA-LIHC","clinical")
#print(clin )
laml = read.maf(
maf,
clinicalData = clinical,
removeDuplicatedVariants = TRUE,
useAll = TRUE,
gisticAllLesionsFile = NULL,
gisticAmpGenesFile = NULL,
gisticDelGenesFile = NULL,
gisticScoresFile = NULL,
cnLevel = "all",
cnTable = NULL,
isTCGA = TRUE,
vc_nonSyn = NULL,
verbose = TRUE
)

Answer 1

You should have: a) loaded with library(maftools) and b) included what was printed out before that error message:
-Validating
-Silent variants: 18306
-Summarizing
--Possible FLAGS among top ten genes:
TTN
MUC16
OBSCN
FLG
-Processing clinical data
Available fields in provided annotations..
[1] "bcr_patient_barcode" "additional_studies"
[3] "tissue_source_site" "patient_id"
# snipped remaining 78 column names
Notice that the first column is not named "Tumor_Sample_Barcode", so you need to follow the helpful error message directions and rename the appropriate column which appears to be the first one:
ns. After doing so I get:
-Validating
-Silent variants: 18306
-Summarizing
--Possible FLAGS among top ten genes:
TTN
MUC16
OBSCN
FLG
-Processing clinical data
-Finished in 1.911s elapsed (2.470s cpu)