bowtie text file on R

Question

[onemore100iq]

How to download http://bowtie-bio.sourceforge.net/recount/countTables/bottomly_count_table.txt in R

I used <download.file> but did not work , no matter I use nothing works

any help is highly appreciated

[Ram]

Hello onemore100iq!

We believe that this post does not fit the main topic of this site.

Not bioinformatics, this is basic browser usage. Right click, save as.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

[onemore100iq]

Hi,

Sorry, for writing my bioinformatics related question in a general form, I was so tired and so frustrated for hours so I just rushed in writing the question in such general mode. But, bowtie-bio link is all about bioinformatics and used in R, and I do not know how to download its data set to run my RNA seq analysis. So, would you please open my question link to get any help to know how to download < http://bowtie-bio.sourceforge.net/recount/countTables/bottomly_count_table.txt > in R so I can run its RNA seq data set.

Thanks in advance

[Ram]

OP, you're looking to read a text file hosted online in R. That is pushing the boundaries of the topics we discuss here, but I will open your question. Please elaborate on what your problem is and what you've tried the next time. For example, you've mentioned only one function you tried - that comes off, from the text of your initial post alone, as a trivial amount of effort invested in trying to solve the problem.

Check out genomax's solution - that should be of help.

[onemore100iq]

Thank you so much.

one of the approaches that I tried is downloading different packages that would help downloading URL on R Also, I tried wget on unix to make sure that the link is really working and it worked on unix but I want to use R/rstudio to get the resulting plots. I will work on genomax's solution now.

Thanks again, highly appreciated

[Michael]

I agree that op is pushing the boundaries of bioinformatics into simple IT question. This is not bioinformatics, and the question should be closed.

Answer 1

[cpad0112]

try following in R:

$ data=read.csv("http://bowtie-bio.sourceforge.net/recount/countTables/bottomly_count_table.txt", header = T,sep="\t", stringsAsFactors = F)

after loading:

> dim(data)
[1] 36536    22

read.csv can read text files from web. Make sure that your R/Rstudio session has access to internet. Rstudio version Version 1.1.383

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 17.10

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale:
 [1] LC_CTYPE=en_IN.UTF-8       LC_NUMERIC=C               LC_TIME=en_IN.UTF-8       
 [4] LC_COLLATE=en_IN.UTF-8     LC_MONETARY=en_IN.UTF-8    LC_MESSAGES=en_IN.UTF-8   
 [7] LC_PAPER=en_IN.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.4.3 tools_3.4.3    yaml_2.1.15

if you are behind the proxy, try following solution at SO: https://stackoverflow.com/questions/6467277/proxy-setting-for-r#8297685 or Rstudio website: https://support.rstudio.com/hc/en-us/articles/200488488-Configuring-R-to-Use-an-HTTP-or-HTTPS-Proxy

[onemore100iq]

It worked, finally after many frustrated hours it worked. Million million thanks cpad0112. very highly appreciated

Answer 2

[GenoMax]

I think this is what the OP is looking for: https://stackoverflow.com/questions/6299220/access-a-url-and-read-data-with-r