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?
- 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.
- 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!