Installing Genomicdatacommon in r

I am installing GenomicDataCommons in R, but when giving following command, getting error as:

GenomicDataCommons::status()

Error in curl::curl_fetch_memory(url, handle = handle) : 
  Could not resolve host: gdc-api.nci.nih.gov

Kindly suggest. Thanks in advance

With regards

genomicdatacommon

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updated 7.7 years ago by lakhujanivijay

• written 7.7 years ago by shivangi.agarwal800

It seems you have successfully installed GenomicDataCommons, and the problem lies in connecting to the GDC API site. Are you behind a firewall / proxy?

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written 7.7 years ago by h.mon

Thanks for your reply. No, there is nothing like that. All other things are working fine.

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written 7.7 years ago by shivangi.agarwal800

1 answer

For matching file id with TCGA barcodes, I am following Kevin post

"Question: problem in matching the names between file names and patients Id in TCGA" C: problem in matching the names between file names and patients Id in TCGA

But getting error. Kindly suggest

Regards

Shivangi

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written 7.7 years ago by shivangi.agarwal800

Resolved the above error by installing the package in R 3.5, but got another error. I followed the commands in Kevin post, all commands ran successfully, but when I was running on my file, it gave error, I ran the commands as :

library(GenomicDataCommons)

manifest <- read.table("a.txt", header=T)

file_uuids <- manifest$id

head(file_uuids)

[1] e01ca3e0-beb0-46b7-bb7c-f5b16f966911 992a7083-28ce-4857-898e-9d4b4fbf2fl1 230082b7-39ec-4fe1-b3c6-daf35458f386 [4] 9bbada51-d827-4eea-af45-47d7b5ba138e db1b68b0-dc0a-48a5-8acb-4cd45ea125e2 5 Levels: 230082b7-39ec-4fe1-b3c6-daf35458f386 ... e01ca3e0-beb0-46b7-bb7c-f5b16f966911

library(GenomicDataCommons)

library(magrittr)

TCGAtranslateID = function(file_ids, legacy = TRUE) { + info = files(legacy = legacy) %>% + filter( ~ file_id %in% file_ids) %>% + select('cases.samples.submitter_id') %>% + results_all() + # The mess of code below is to extract TCGA barcodes + # id_list will contain a list (one item for each file_id) + # of TCGA barcodes of the form 'TCGA-XX-YYYY-ZZZ' + id_list = lapply(info$cases,function(a) { + a[[1]][[1]][[1]]}) + # so we can later expand to a data.frame of the right size + barcodes_per_file = sapply(id_list,length) + # And build the data.frame + return(data.frame(file_id = rep(ids(info),barcodes_per_file), + submitter_id = unlist(id_list))) + }

res = TCGAtranslateID(file_uuids)

res [1] file_id <0 rows> (or 0-length row.names)

contents n a.txt (I placed initially only five ids in a.txt)

e01ca3e0-beb0-46b7-bb7c-f5b16f966911

992a7083-28ce-4857-898e-9d4b4fbf2fl1

230082b7-39ec-4fe1-b3c6-daf35458f386

9bbada51-d827-4eea-af45-47d7b5ba138e

db1b68b0-dc0a-48a5-8acb-4cd45ea125e2

Please suggest.

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written 7.7 years ago by shivangi.agarwal800