Mr. Heiberger, I followed your argument and it works. I received the same data. And yes, ICGC breakes their datasets into separate files based on data type. Thank you for the pointer on selecting all 50 rows, as I assumed that the entirety of gene expression data within the data set would be downloaded through the process you followed, as it does when directly downloading the file via a tsv.gz download.
On Thu, Dec 27, 2018 at 4:05 PM Richard M. Heiberger <r...@temple.edu> wrote: > I downloaded the Donors dataset > > > https://dcc.icgc.org/search?filters=%7B%22donor%22:%7B%22projectId%22:%7B%22is%22:%5B%22GBM-US%22%5D%7D,%22availableDataTypes%22:%7B%22is%22:%5B%22pexp%22%5D%7D%7D%7D > > by clicking "Export table as TSV". > > Then I read it with > > donors <- read.delim("~/Downloads/donors_2018_12_27_03_52_03.tsv") > > Here is the transcript. > > > donors <- read.delim("~/Downloads/donors_2018_12_27_03_52_03.tsv") > > donors > Donor.ID Project.Code Primary.Site Gender Age.at.Diagnosis > 1 DO10892 GBM-US Brain Female 45 > 2 DO12328 GBM-US Brain Male 56 > 3 DO11657 GBM-US Brain Female 73 > 4 DO13510 GBM-US Brain Female 63 > 5 DO12670 GBM-US Brain Female 63 > 6 DO11501 GBM-US Brain Female 59 > 7 DO13809 GBM-US Brain Female 74 > 8 DO13647 GBM-US Brain Male 56 > 9 DO11645 GBM-US Brain Male 73 > 10 DO14145 GBM-US Brain Female 85 > Tumor.Stage.at.Diagnosis Survival.Time..days. SSM CNSM STSM SGV > METH.A > 1 NA NA True True False False > True > 2 NA 154 True True False False > True > 3 NA NA True True False False > True > 4 NA 1448 True True False False > True > 5 NA 772 True True False False > True > 6 NA NA True True False False > True > 7 NA 213 True True False False > True > 8 NA 383 True True False False > True > 9 NA 113 True True False False > True > 10 NA 94 True True False False > True > METH.S EXP.A EXP.S PEXP miRNA.S JCN Mutations Mutated.Genes > 1 False True True True False False 269 392 > 2 False True False True False False 192 263 > 3 False True False True False False 128 209 > 4 False True True True False False 130 199 > 5 False True True True False False 142 194 > 6 False True True True False False 129 190 > 7 False True False True False False 130 178 > 8 False True False True False False 116 175 > 9 False True False True False False 125 174 > 10 False True True True False False 108 169 > > > > I don't know how to get the download of the whole file. It looks like you > could page through it with the page menu at the bottom of the webpage. If > you do that, set it for 50 at a time instead of the default 10. > > For the Genes and the two types of Mutation files, it will be more > nuisance this way because there are about 10000 rows for each of those > three files, thus about 200 of these statements per dataset. > > I think it is time to move to the bioconductor list for specific guidance > on this type of dataset. > > > On Thu, Dec 27, 2018 at 3:28 PM Spencer Brackett < > spbracket...@saintjosephhs.com> wrote: > >> Mr. Calboli, >> >> After beginning to unpack the GBM file you sent me via directly importing >> it unit my console, I received the following: >> >> View(GBM_PEXP.tsv) >> >> **Note that I named the file GBM_PEXP.tsv)** >> >> Upon downloading, my script now contains a 2 by 2 table, with the x >> column still containing encoded script. As for my Data summary to the >> right, this new file reports that 2 objects are acting upon 1 variable. >> How should I proceed? >> >> -Spencer >> >> On Thu, Dec 27, 2018 at 3:12 PM Federico Calboli < >> federico.calb...@kuleuven.be> wrote: >> >> > Unpack these files. >> > >> > F >> > >> > >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
