dplyr::bind_rows(): ! Can't combine ..368$Tumor_Seq_Allele2 and ..369$Tumor_Seq_Allele2 .One error problem occurred caused by data type during using GDCprepare to handle BRCA data

[Lancelof2019]

I found one problem when I tried to download the data:

Error in dplyr::bind_rows(): ! Can't combine ..368$Tumor_Seq_Allele2 and ..369$Tumor_Seq_Allele2 .

Whether is this a problem in the GDC lib function?

I can use this function to handle the data from TCGA-BLCA and TCGA-SKCM.

But I met this problem when I handle the TCGA-BRCA.

Could you please provide any suggestion and solution?

The code can seen below:

query <- GDCquery(
project = paste0("TCGA-", cancer_type),
data.category = "Simple Nucleotide Variation",
access = "open",
data.type = "Masked Somatic Mutation",
#workflow.type = "MuSE Variant Aggregation and Masking"
workflow.type = "Aliquot Ensemble Somatic Variant Merging and Masking"
)
GDCdownload(query)
maf <- GDCprepare(query)
The issue came out when the statement runs at maf <- GDCprepare(query)

I checked the data structure:

But I don't know which part includes the combining two" 368$Tumor_Seq_Allele2 (character)" and "..369$Tumor_Seq_Allele2 (logical)".

https://www.biostars.org/p/9593443/

[Rmulet]

I have the same issue with TARGET-AML and TARGET-ALL-P2 (probably others as well, but I have only tested those). The error seems confined to "Masked Somatic Mutation" data only.

[Lancelof2019]

I found the same issue happened in TCGA - BRCA,ESCA and PAAD.

Error in dplyr::bind_rows():
! Can't combine ..26$Tumor_Seq_Allele2 and ..27$Tumor_Seq_Allele2 .
Run rlang::last_trace() to see where the error occurred

[tiagochst]

Hi,

Could you try the github version, please? TCGA-ESCA and TCGA-BRCA are working on my side.
BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")

[Lancelof2019]

Hi,

Could you try the github version, please? TCGA-ESCA and TCGA-BRCA are working on my side. BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")

Should I remove the old version of TCGA links and install the latest version?

[tiagochst]

The old version will be overwritten with the new one. You just need to 1. install the latest version with BiocManager::install("BioinformaticsFMRP/ TCGAbiolinks") 2. restart R 3. Load the new version with library(TCGAbiolinks)

…

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