library("TCGAbiolinks")
library("dplyr")
library("DT")
library("SummarizedExperiment")
cancer_type <- "TCGA-LUAD"
data_type <- "Gene Expression Quantification"
data_category <- "Transcriptome Profiling"
workflow_type <- "HTSeq - FPKM"
Expr_df <- GDCquery(project = cancer_type,
data.category = data_category,
data.type = data_type,
workflow.type = workflow_type)
GDCdownload(Expr_df,method = "api",files.per.chunk = 6)
expdat<- GDCprepare(query = Expr_df)
报错如下
> expdat<- GDCprepare(query = Expr_df)
|================================================================================|100% Completed after 57 s
Starting to add information to samples
=> Add clinical information to samples
=> Adding TCGA molecular information from marker papers
=> Information will have prefix 'paper_'
luad subtype information from:doi:10.1038/nature13385
From the 60483 genes we couldn't map 3881
Error in MatrixGenerics:::.load_next_suggested_package_to_search(x) :
Failed to find a rowRanges() method for RangedSummarizedExperiment objects.
请问该如何解决?
检查是不是TCGAbiolinks版本问题,卸载后通过BiocManager安装一下试试。
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("TCGAbiolinks")