[R] you are making it far too difficult

[Spencer Brackett]

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 <rmh using 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 <
> spbrackett20 using 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.calboli using kuleuven.be> wrote:
>>
>> > Unpack these files.
>> >
>> > F
>> >
>> >
>>
>>         [[alternative HTML version deleted]]
>>
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>>
>

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