[R] Loading large tar.gz XenaHub Data into R

[Bert Gunter]

These are gzipped files, I assume. So see ?gzfile and associated info
for how to open a gzip connection and read from it. You may also
prefer to search (e.g. at rseek.org) on "read a gzipped file" or
similar for possible alternatives.

Of course, if they're not gzipped files, then ignore the above. If
they are, your current approach is hopeless.


Cheers,
Bert

On Thu, Aug 1, 2019 at 3:13 PM Spencer Brackett
<spbrackett20 using saintjosephhs.com> wrote:
>
> Good evening,
>
> I am attempting to load the following Xena dataset
> https://tcga.xenahubs.net/download/TCGA.GBMLGG.sampleMap/HumanMethylation450.gz
>
> I am trying to unpack the dataset and read it into R as a table, but due to
> the size of the file, I am having some trouble. The following are the
> commands I have tried thus far.
>
> HumanMethylation450 <- fread("
> https://tcga.xenahubs.net/download/TCGA.GBMLGG.sampleMap/HumanMethylation450.gz
> ")
>
> readLines("
> https://tcga.xenahubs.net/download/TCGA.GBMLGG.sampleMap/HumanMethylation450.gz
> ")
>
>                  ###These two above attempts failed with warning messages
> from R###
>
> Methyl <-read.delim("
> https://tcga.xenahubs.net/download/TCGA.GBMLGG.sampleMap/HumanMethylation450.gz
> ")
>
>                ##This attempt is still processing, but has been doing so
> for quite some time##
>
> Any ideas as to what else I could try?
>
> Best,
>
> Spencer
>
>         [[alternative HTML version deleted]]
>
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