[R] Using read.table for importing gz file

[David Winsemius]

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 using comcast.net <mailto:dwinsemius using 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]]
>     >
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