Error: 'GDCquery_Maf' is not an exported object from 'namespace:TCGAbiolinks

Question

I have already installed sesame and TCGAbiolinks,but the error came out with Error: 'GDCquery_Maf' is not an exported object from 'namespace:TCGAbiolinks ,I am not quite sure how to solve it. Can anyone give any suggestions?

options(stringsAsFactors = F)
library(TCGAbiolinks)
library(SummarizedExperiment)
library(limma)
library(biomaRt)
library(TCGAbiolinks)
library(sesame)

>   mty_assay <- as.data.frame(assay(data_mty)) # DNA methylation matrix
>   mty_colData <- as.data.frame(colData(data_mty)) # Patient annotation(475 patients)
>   
>   filename <- paste0("./data/tcga_data/", cancer_type, "_mty_colData.RData")
>   
>   #saveRDS(mty_colData, "./data/tcga_data/mty_colData.RData")
>   
>   saveRDS(mty_colData, filename)
>   
>   mty_rowRanges <- as.data.frame(rowRanges(data_mty)) # cg probe annotation
>   
>   #### Collect gene mutation data
>   #maf <- GDCquery_Maf("SKCM", pipelines = "muse") # Mutation annotation#error information:4444444444444444444444444444444444444
>   maf <- TCGAbiolinks::GDCquery_Maf(cancer_type, pipelines = "muse") # Mutation a
Error: 'GDCquery_Maf' is not an exported object from 'namespace:TCGAbiolinks'

Answer 1

I found the solution,the maf function 'GDCquery_Maf' has been removed from TCGAbolinks.

https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/511

I use the below instead.

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