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BioinformaticsFMRP / TCGAbiolinks

TCGAbiolinks
http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html
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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

Open Lancelof2019 opened 2 months ago

Lancelof2019 commented 2 months ago

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 commented 2 months ago

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 commented 2 months ago

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 commented 2 months ago

Hi,

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

Lancelof2019 commented 2 months ago

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 commented 2 months ago

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?

— Reply to this email directly, view it on GitHub https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/627#issuecomment-2084466892, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABDQ6M5SLSF67OROUV3PW3Y742DZAVCNFSM6AAAAABGXDX5JKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBUGQ3DMOBZGI . You are receiving this because you commented.Message ID: @.***>