How to set up TCGAbiolinks in R studio?
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4.8 years ago
elizabethR ▴ 70

Hey

I am trying to set up TCGABiolinks in R studio, starting by downloading and collating data and then doing differential expression analysis of RNASeq results. I have a good idea after extensive research of what I need to do to analyse my data and have read the manual many times. However I have two problems thats stopping me in trying to set this up. Could anyone please help?

1. Ive downloaded and opened the package TCGA biolinks. Ive located the TCGA Assembler file that I need to access and download the data. I managed to set the working directory to this folder as advised in the manual but when I try to source Modules A and B I get repeated errors:

I type > source("./Module_A.r")

It tells me "Error in file(filename, "r", encoding = encoding) : cannot open the connection In addition: Warning message: In file(filename, "r", encoding = encoding) : cannot open file './Module_A.r': No such file or directory"

Ive tried every variation of the command file like removing the underscore and the r suffix and still get the same problem. Looking in the actual folder there are no r files theyre all m files. What am I doing wrong? My understanding is I need to source these folders to allow me to then undertake the next steps.

1. The second problem is regarding traverseresultfile. My understanding is that I need to set this up to allow the computer to identify the datasets I will then query and subsequently tell it to download. There is no clear instruction on how to create one of these. The traverseresultfile in Module A is from 2013 so desperately needs updating. Can anyone help me with this?

Many many thanks for any help or advice you can give me. Im at my wits end!

RNA-Seq R • 4.0k views
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TCGAbiolinks (https://www.bioconductor.org/packages/release/bioc/vignettes/TCGAbiolinks/inst/doc/tcgaBiolinks.html) and TCGA Assembler (http://www.compgenome.org/TCGA-Assembler/) are two different package. TCGAbiolinks is very easy to use than TCGA-Assembler. For TCGA-Assembler you need to install some other dependent packages.

I tried and its working:

setwd("/Users/aa/xxx//TCGA-Assembler")
install.packages("httr_0.5.tar.gz")
library(HGNChelper)
source("./Module_A.r");
source("./Module_B.r");

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Thank you Mike :) It is now telling me that httr_0.5.tar.gz is not available for r studio version 3.2.5. Are there other variants of that file for different versions and where may I find them? Im not certain I understand where httr_0.5 tar file is sourcing from

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what is problem in TCGAbiolinks? which is much easier and well explained manual.

install.packages("httr_0.5.tar.gz")

https://cran.r-project.org/src/contrib/Archive/httr/

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4.6 years ago

I personally use TCGAbiolinks. It works fine and it is much simpler than the other packages, also now that they changed downloading server (GDC)

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4.6 years ago
EagleEye 6.8k

Since TCGA has been recently moved to new GDC portal, TCGA-Assembler is out of service. But TCGAbiolinks has been updated to support new GDC portal, still for some of the functions work is in progress.

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4.0 years ago
woodhaha • 0

The TCGA assembler pkg has also updated you can try the new version