Hello,
I am trying to read the following Xena dataset into R for data analysis:
https://tcga.xenahubs.net/download/TCGA.GBMLGG.sampleMap/HumanMethylation450.gz
I tried to run the following
read.table(gzfile("HumanMethylation450.gz")),
but R ended up crashing as a result.
Is there perhaps a way to use read.table with fread in some way to do this?
Many thanks,
Spencer
[[alternative HTML version deleted]]
Unsubscribe On Sat, 10 Aug 2019 at 20:30, Spencer Brackett < spbrackett20 at saintjosephhs.com> wrote:> Hello, > > I am trying to read the following Xena dataset into R for data analysis: > > https://tcga.xenahubs.net/download/TCGA.GBMLGG.sampleMap/HumanMethylation450.gz > > I tried to run the following read.table(gzfile("HumanMethylation450.gz")), > but R ended up crashing as a result. > > Is there perhaps a way to use read.table with fread in some way to do this? > > Many thanks, > > Spencer > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at 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]]
Have you tried using readLines in the manner illustrated on the ?gzfile help page? David. On 8/10/19 12:29 PM, Spencer Brackett wrote:> Hello, > > I am trying to read the following Xena dataset into R for data analysis: > https://tcga.xenahubs.net/download/TCGA.GBMLGG.sampleMap/HumanMethylation450.gz > > I tried to run the following read.table(gzfile("HumanMethylation450.gz")), > but R ended up crashing as a result. > > Is there perhaps a way to use read.table with fread in some way to do this? > > Many thanks, > > Spencer > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at 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.
Well, let's see about "rules"? ... you posted in HTML when this is
a
plain text mailing list and then you replied to only me when you are
supposed reply to the list (so I'm putting back the list address in my
reply:
When I copied your code and then attempted to do a bit of debugging I get:
> z <-
readLines(gzcon(url(?https://TCGA.xenahubs.net/download/TCGA.GBMLGG.sampleMap/HumanMethylation450.gz?)),
n = 100)
Error: unexpected input in "z <- readLines(gzcon(url(?"
# that was because you had "smart-quotes" rather than ASCII quotes:
> z <- readLines(gzcon(url(
'https://TCGA.xenahubs.net/download/TCGA.GBMLGG.sampleMap/HumanMethylation450.gz'
)), n = 100)
> z[1:10]
?[1]
"sample\tTCGA-E1-5319-01\tTCGA-HT-7693-01\tTCGA-CS-6665-01\tTCGA-S9-A7J2-01\tTCGA-FG-A6J3-01\tTCGA-FG-6688-01\tTCGA-S9-A6TX-01\tTCGA-VM-A8C8-01\tTCGA-74-6577-01\tTCGA-06-AABW-11\tTCGA-06-0125-02\tTCGA-HT-A74L-01\tTCGA-26-A7UX-01\tTCGA-DU-A5TS-01\tTCGA-06-6388-01\tTCGA-DB-A4XA-01\tTCGA-06-A7TL-01\tTCGA-HT-A4DV-01\tTCGA-TQ-A7RP-01\tTCGA-E1-5311-01\tTCGA-28-5213-01\tTCGA-E1-A7YI-01\tTCGA-E1-5305-01\tTCGA-F6-A8O4-01\tTCGA-HT-8113-01\tTCGA-DH-A66G-01\tTCGA-76-4932-01\t
Snipped hundreds of lines. So this seems to indicate that this is a tab
separated file. Don't you have some documentation to refer to?
This seems possibly useful:
> z <- read.table(
text=readLines(gzcon(url('https://TCGA.xenahubs.net/download/TCGA.GBMLGG.sampleMap/HumanMethylation450.gz')),
n = 100), header=TRUE, sep="\t")
> str(z)
'data.frame':??? 99 obs. of? 686 variables:
?$ sample???????? : Factor w/ 99 levels
"cg00036732","cg00651829",..:
53 2 60 41 16 13 37 20 70 21 ...
?$ TCGA.E1.5319.01: num? 0.4019 0.0215 0.053 0.0453 0.515 ...
?$ TCGA.HT.7693.01: num? 0.9364 0.0216 0.0547 0.0819 0.6129 ...
?$ TCGA.CS.6665.01: num? 0.0345 0.0164 0.0719 0.0497 0.6648 ...
?$ TCGA.S9.A7J2.01: num? 0.0295 0.0168 0.0421 0.0867 0.1657 ...
?$ TCGA.FG.A6J3.01: num? 0.0248 0.0161 0.0556 0.0902 0.5042 ...
?$ TCGA.FG.6688.01: num? 0.0203 0.0179 0.0321 0.0513 0.1075 ...
?$ TCGA.S9.A6TX.01: num? 0.0378 0.0199 0.0623 0.0992 0.7662 ...
?$ TCGA.VM.A8C8.01: num? 0.0271 0.0172 0.0466 0.0564 0.3478 ...
?$ TCGA.74.6577.01: num? 0.0237 0.0193 0.0196 0.0961 0.1242 ...
?$ TCGA.06.AABW.11: num? 0.0323 0.0156 0.0395 0.0708 0.1136 ...
?$ TCGA.06.0125.02: num? 0.0238 0.0181 0.039 0.068 0.0796 ...
?$ TCGA.HT.A74L.01: num? 0.7409 0.0221 0.0596 0.0765 0.8157 ...
#snipped the output
# there seemed to be 686 columns
--
David.
On 8/10/19 3:07 PM, Spencer Brackett wrote:> I?ve tried z <-
>
readLines(gzcon(url(?https://TCGA.xenahubs.net/download/TCGA.GBMLGG.sampleMap/HumanMethylation450.gz?)),
> n = 100)
>
> Which prints out the indicated 10 rows, but I can not seem to run the
> same code excluding the n = 100 without R stalling and me being forced
> to close the program. All I am trying to do is ensure that the whole
> file is imported into R so that I can proceed with a survival analysis.
>
> Also, what particular rule of the mailing list did I break? I
> apologize in advance, as I thought that code specific queries like the
> one I asked were acceptable.
>
> Many thanks,
>
> Spencer
>
> On Sat, Aug 10, 2019 at 5:51 PM David Winsemius
> <dwinsemius at comcast.net <mailto:dwinsemius at comcast.net>>
wrote:
>
> Have you tried using readLines in the manner illustrated on the
> ?gzfile
> help page?
>
>
> David.
>
> On 8/10/19 12:29 PM, Spencer Brackett wrote:
> > Hello,
> >
> > I am trying to read the following Xena dataset into R for data
> analysis:
> >
>
https://tcga.xenahubs.net/download/TCGA.GBMLGG.sampleMap/HumanMethylation450.gz
> >
> > I tried to run the following
> read.table(gzfile("HumanMethylation450.gz")),
> > but R ended up crashing as a result.
> >
> > Is there perhaps a way to use read.table with fread in some way
> to do this?
> >
> > Many thanks,
> >
> > Spencer
> >
> >? ? ? ?[[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help at r-project.org <mailto:R-help at 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.
>
Further note:
After three minutes of waiting? ... not a particularly long wait in my
opinion, I get this:
> z <- read.table(
text=readLines(gzcon(url('https://TCGA.xenahubs.net/download/TCGA.GBMLGG.sampleMap/HumanMethylation450.gz'))
), header=TRUE, sep="\t")
> dim(z)
[1] 485577??? 686
So almost half a million lines of data in a rather wide dataset for an
incompletely described file.
I'd say R seems to be "working" properly.
data.table::fread was more informative about the process but acheived
basically the same result in 1/6th the time:
??fread
system.time( z <-
fread('https://TCGA.xenahubs.net/download/TCGA.GBMLGG.sampleMap/HumanMethylation450.gz',
sep="\t")? )
#-----------
[100%] Downloaded 597770433 bytes...
?? user? system elapsed
?20.682?? 3.322? 29.292
> dim(z)
[1] 485577??? 686
--
David.
On 8/10/19 5:32 PM, David Winsemius wrote:> Well, let's see about "rules"? ... you posted in HTML when
this is a
> plain text mailing list and then you replied to only me when you are
> supposed reply to the list (so I'm putting back the list address in my
> reply:
>
>
> When I copied your code and then attempted to do a bit of debugging I
> get:
>
>
> > z <-
>
readLines(gzcon(url(?https://TCGA.xenahubs.net/download/TCGA.GBMLGG.sampleMap/HumanMethylation450.gz?)),
> n = 100)
> Error: unexpected input in "z <- readLines(gzcon(url(?"
>
> # that was because you had "smart-quotes" rather than ASCII
quotes:
>
>
> > z <- readLines(gzcon(url(
>
'https://TCGA.xenahubs.net/download/TCGA.GBMLGG.sampleMap/HumanMethylation450.gz'
> )), n = 100)
> > z[1:10]
> ?[1]
>
"sample\tTCGA-E1-5319-01\tTCGA-HT-7693-01\tTCGA-CS-6665-01\tTCGA-S9-A7J2-01\tTCGA-FG-A6J3-01\tTCGA-FG-6688-01\tTCGA-S9-A6TX-01\tTCGA-VM-A8C8-01\tTCGA-74-6577-01\tTCGA-06-AABW-11\tTCGA-06-0125-02\tTCGA-HT-A74L-01\tTCGA-26-A7UX-01\tTCGA-DU-A5TS-01\tTCGA-06-6388-01\tTCGA-DB-A4XA-01\tTCGA-06-A7TL-01\tTCGA-HT-A4DV-01\tTCGA-TQ-A7RP-01\tTCGA-E1-5311-01\tTCGA-28-5213-01\tTCGA-E1-A7YI-01\tTCGA-E1-5305-01\tTCGA-F6-A8O4-01\tTCGA-HT-8113-01\tTCGA-DH-A66G-01\tTCGA-76-4932-01\t
>
> Snipped hundreds of lines. So this seems to indicate that this is a
> tab separated file. Don't you have some documentation to refer to?
>
>
> This seems possibly useful:
>
>
> > z <- read.table(
>
text=readLines(gzcon(url('https://TCGA.xenahubs.net/download/TCGA.GBMLGG.sampleMap/HumanMethylation450.gz')),
> n = 100), header=TRUE, sep="\t")
> > str(z)
> 'data.frame':??? 99 obs. of? 686 variables:
> ?$ sample???????? : Factor w/ 99 levels
"cg00036732","cg00651829",..:
> 53 2 60 41 16 13 37 20 70 21 ...
> ?$ TCGA.E1.5319.01: num? 0.4019 0.0215 0.053 0.0453 0.515 ...
> ?$ TCGA.HT.7693.01: num? 0.9364 0.0216 0.0547 0.0819 0.6129 ...
> ?$ TCGA.CS.6665.01: num? 0.0345 0.0164 0.0719 0.0497 0.6648 ...
> ?$ TCGA.S9.A7J2.01: num? 0.0295 0.0168 0.0421 0.0867 0.1657 ...
> ?$ TCGA.FG.A6J3.01: num? 0.0248 0.0161 0.0556 0.0902 0.5042 ...
> ?$ TCGA.FG.6688.01: num? 0.0203 0.0179 0.0321 0.0513 0.1075 ...
> ?$ TCGA.S9.A6TX.01: num? 0.0378 0.0199 0.0623 0.0992 0.7662 ...
> ?$ TCGA.VM.A8C8.01: num? 0.0271 0.0172 0.0466 0.0564 0.3478 ...
> ?$ TCGA.74.6577.01: num? 0.0237 0.0193 0.0196 0.0961 0.1242 ...
> ?$ TCGA.06.AABW.11: num? 0.0323 0.0156 0.0395 0.0708 0.1136 ...
> ?$ TCGA.06.0125.02: num? 0.0238 0.0181 0.039 0.068 0.0796 ...
> ?$ TCGA.HT.A74L.01: num? 0.7409 0.0221 0.0596 0.0765 0.8157 ...
>
> #snipped the output
>
> # there seemed to be 686 columns
>
>