One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
0
0
Entering edit mode
@6706785b
Last seen 11 weeks ago
Finland

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

Error in dplyr::bind_rows(): ! Can't combine ..368$Tumor_Seq_Allele2 <character> and ..369$Tumor_Seq_Allele2 <logical>. Is this a problem in the GDC lib function?

When I use this function to handle the data from TCGA-BLCA and TCGA-SKCM, there is no problem.

But I met this problem when I handle the data from 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 this statement runs: 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).

  Hugo_Symbol = col_character(),
  Entrez_Gene_Id = col_double(),
  Center = col_character(),
  NCBI_Build = col_character(),
  Chromosome = col_character(),
  Start_Position = col_double(),
  End_Position = col_double(),
  Strand = col_character(),
  Variant_Classification = col_character(),
  Variant_Type = col_character(),
  Reference_Allele = col_character(),
  Tumor_Seq_Allele1 = col_character(),
  Tumor_Seq_Allele2 = col_character(),
  dbSNP_RS = col_character(),
  dbSNP_Val_Status = col_logical(),
  Tumor_Sample_Barcode = col_character(),
  Matched_Norm_Sample_Barcode = col_character(),
  Match_Norm_Seq_Allele1 = col_logical(),
  Match_Norm_Seq_Allele2 = col_logical(),
  Tumor_Validation_Allele1 = col_logical(),
  Tumor_Validation_Allele2 = col_logical(),
  Match_Norm_Validation_Allele1 = col_logical(),
  Match_Norm_Validation_Allele2 = col_logical(),
  Verification_Status = col_logical(),
  Validation_Status = col_logical(),
  Mutation_Status = col_character(),
  Sequencing_Phase = col_logical(),
  Sequence_Source = col_logical(),
  Validation_Method = col_logical(),
  Score = col_logical(),
  BAM_File = col_logical(),
  Sequencer = col_logical(),
  Tumor_Sample_UUID = col_character(),
  Matched_Norm_Sample_UUID = col_character(),
  HGVSc = col_character(),
  HGVSp = col_character(),
  HGVSp_Short = col_character(),
  Transcript_ID = col_character(),
  Exon_Number = col_character(),
  t_depth = col_double(),
  t_ref_count = col_double(),
  t_alt_count = col_double(),
  n_depth = col_double(),
  n_ref_count = col_logical(),
  n_alt_count = col_logical(),
  all_effects = col_character(),
  Allele = col_character(),
  Gene = col_character(),
  Feature = col_character(),
  Feature_type = col_character(),
  One_Consequence = col_character(),
  Consequence = col_character(),
  cDNA_position = col_character(),
  CDS_position = col_character(),
  Protein_position = col_character(),
  Amino_acids = col_character(),
  Codons = col_character(),
  Existing_variation = col_character(),
  DISTANCE = col_logical(),
  TRANSCRIPT_STRAND = col_double(),
  SYMBOL = col_character(),
  SYMBOL_SOURCE = col_character(),
  HGNC_ID = col_character(),
  BIOTYPE = col_character(),
  CANONICAL = col_character(),
  CCDS = col_character(),
  ENSP = col_character(),
  SWISSPROT = col_character(),
  TREMBL = col_character(),
  UNIPARC = col_character(),
  UNIPROT_ISOFORM = col_character(),
  RefSeq = col_character(),
  MANE = col_character(),
  APPRIS = col_character(),
  FLAGS = col_logical(),
  SIFT = col_character(),
  PolyPhen = col_character(),
  EXON = col_character(),
  INTRON = col_logical(),
  DOMAINS = col_character(),
  `1000G_AF` = col_double(),
  `1000G_AFR_AF` = col_double(),
  `1000G_AMR_AF` = col_double(),
  `1000G_EAS_AF` = col_double(),
  `1000G_EUR_AF` = col_double(),
  `1000G_SAS_AF` = col_double(),
  ESP_AA_AF = col_double(),
  ESP_EA_AF = col_double(),
  gnomAD_AF = col_double(),
  gnomAD_AFR_AF = col_double(),
  gnomAD_AMR_AF = col_double(),
  gnomAD_ASJ_AF = col_double(),
  gnomAD_EAS_AF = col_double(),
  gnomAD_FIN_AF = col_double(),
  gnomAD_NFE_AF = col_double(),
  gnomAD_OTH_AF = col_double(),
  gnomAD_SAS_AF = col_double(),
  MAX_AF = col_double(),
  MAX_AF_POPS = col_character(),
  gnomAD_non_cancer_AF = col_double(),
  gnomAD_non_cancer_AFR_AF = col_double(),
  gnomAD_non_cancer_AMI_AF = col_double(),
  gnomAD_non_cancer_AMR_AF = col_double(),
  gnomAD_non_cancer_ASJ_AF = col_double(),
  gnomAD_non_cancer_EAS_AF = col_double(),
  gnomAD_non_cancer_FIN_AF = col_double(),
  gnomAD_non_cancer_MID_AF = col_double(),
  gnomAD_non_cancer_NFE_AF = col_double(),
  gnomAD_non_cancer_OTH_AF = col_double(),
  gnomAD_non_cancer_SAS_AF = col_double(),
  gnomAD_non_cancer_MAX_AF_adj = col_double(),
  gnomAD_non_cancer_MAX_AF_POPS_adj = col_character(),
  CLIN_SIG = col_character(),
  SOMATIC = col_character(),
  PUBMED = col_logical(),
  TRANSCRIPTION_FACTORS = col_logical(),
  MOTIF_NAME = col_logical(),
  MOTIF_POS = col_logical(),
  HIGH_INF_POS = col_logical(),
  MOTIF_SCORE_CHANGE = col_logical(),
  miRNA = col_logical(),
  IMPACT = col_character(),
  PICK = col_double(),
  VARIANT_CLASS = col_character(),
  TSL = col_double(),
  HGVS_OFFSET = col_double(),
  PHENO = col_character(),
  GENE_PHENO = col_double(),
  CONTEXT = col_character(),
  tumor_bam_uuid = col_character(),
  normal_bam_uuid = col_character(),
  case_id = col_character(),
  GDC_FILTER = col_logical(),
  COSMIC = col_character(),
  hotspot = col_character(),
  RNA_Support = col_character(),
  RNA_depth = col_logical(),
  RNA_ref_count = col_logical(),
  RNA_alt_count = col_logical(),
  callers = col_character()

enter image description here

GDCRNATools TCGA • 218 views
ADD COMMENT

Login before adding your answer.

Traffic: 705 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6