CPTAC data download

Question

[Rob]

Hi friends

Is there an R code to download CPTAC mutation data? I tried to use the following code but it did not work. I would appreciate your help. Thanks

install.packages("tidyverse")
library(tidyverse)
if (!require("BiocManager"))
    install.packages("BiocManager")
BiocManager::install('GenomicDataCommons')
library(GenomicDataCommons)

qfiles = files() %>% filter( ~ cases.project.project_id == 'CPTAC-3-kirc' &
                            type == 'mutation' &
                            access == "open" #&
                            #analysis.workflow_type == 'STAR - Counts'
                              )
manifest_df = qfiles %>% manifest() # I got error here
nrow(manifest_df)

The error I get is : Error in if (ncol(tmp) < 5) { : argument is of length zero

[Ram]

1. What do you mean "it did not work"? You need to give us as much detail as you can
2. Your code is incomplete. What is files()? What libraries do you have loaded? Add the output to sessionInfo().

[Rob]

Hi thanks for responding. here is the full code with libraries and packages. file here is all the data before filtering for only mutation.

install.packages("tidyverse")
library(tidyverse)
if (!require("BiocManager"))
    install.packages("BiocManager")
BiocManager::install('GenomicDataCommons')
library(GenomicDataCommons)

qfiles = files() %>% filter( ~ cases.project.project_id == 'CPTAC-3-kirc' &
                            type == 'mutation' &
                            access == "open" #&
                            #analysis.workflow_type == 'STAR - Counts'
                              )
manifest_df = qfiles %>% manifest() # I got error here
nrow(manifest_df)

The error I get is : Error in if (ncol(tmp) < 5) { : argument is of length zero

[Ram]

I've moved the relevant content to your post. You've still not explained where files() comes from and you've also not added the output to sessionInfo() yet.