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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 #627
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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. |
I found the same issue happened in TCGA - BRCA,ESCA and PAAD. Error in dplyr::bind_rows(): |
Hi, Could you try the github version, please? TCGA-ESCA and TCGA-BRCA are working on my side. |
Should I remove the old version of TCGA links and install the latest version? |
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)
…On Tue, Apr 30, 2024 at 2:22 AM Lance ***@***.***> wrote:
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?
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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/
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