Re: [R] Using read.table for importing gz file

2019-08-11 Thread J H
Unsubscribe On Sat, 10 Aug 2019 at 20:30, Spencer Brackett < spbracket...@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 foll

Re: [R] Using read.table for importing gz file

2019-08-10 Thread David Winsemius
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 S

Re: [R] Using read.table for importing gz file

2019-08-10 Thread 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:

Re: [R] Using read.table for importing gz file

2019-08-10 Thread David Winsemius
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.

[R] Using read.table for importing gz file

2019-08-10 Thread Spencer Brackett
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 t