Gdcprepare() error.

Question

[Harshvardhan]

I’m really struggling with this and I need urgent help.

I keep running the following code but after the gdcprepare function, it either crashes my computer or freezes the console. I have no idea what to do, someone please help.

library("TCGAbiolinks", quietly = T)
library("limma", quietly = T)
library("edgeR", quietly = T)
library("glmnet", quietly = T)
library("factoextra", quietly = T)
library("FactoMineR", quietly = T)
library("caret", quietly = T)
library("SummarizedExperiment", quietly = T)
library("gplots", quietly = T)
library("survival", quietly = T)
library("survminer", quietly = T)
library("RColorBrewer", quietly = T)
library("gProfileR", quietly = T)
library("genefilter", quietly = T)

## Acess GDC and get info on projects

GDCprojects = getGDCprojects()

View(GDCprojects[c("project_id", "name")])

# get details of the Kidney cancer project
TCGAbiolinks:::getProjectSummary("TCGA-KIRC")

## Query GDC for RNAseq data from KIRC dataset for primary tumor and normal tissue
query_TCGA_KIRC = GDCquery(
  project = "TCGA-KIRC",
  data.category = "Transcriptome Profiling",
  access = "open",
  experimental.strategy = "RNA-Seq",
  workflow.type = "HTSeq - Counts",
  sample.type =c("Primary Tumor", "Solid Tissue Normal"))

#      make results as table
all_res = getResults(query_TCGA_KIRC) 
colnames(all_res)

# how many samples in each sample type
table(factor(all_res$sample_type)) 

## Download the files specified in the query.

GDCdownload(query = query_TCGA_KIRC) # rerun if download fails


### Prepare the downloaded data and other associated data into an object
## load the actual RNASeq data into R
## both clinical and expression data will be present in this object

tcga_data = GDCprepare(query_TCGA_KIRC)
View(tcga_data)

# Clinical data can be accessed using the colData() function
colnames(colData(tcga_data))

table(tcga_data@colData$primary_diagnosis)  
table(tcga_data@colData$vital_status)
table(tcga_data@colData$definition)

# RNAseq data can be accessed using the assay() function
dim(assay(tcga_data))     # gene expression matrices.
head(assay(tcga_data)[,1:6]) # expression of first 6 genes and first 6 samples
head(rowData(tcga_data))     # ensembl id and gene id of the first 6 genes. 


# Save the data as a file
saveRDS(object = tcga_data,
        file = "tcga_data.RDS",
        compress = FALSE)

[Ram]

Are you running this on RStudio? Does the GDCprepare run to completion or does the crash happen before it's done running?