Data import with read.delim
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@justinkablan225-18560
Last seen 2.2 years ago

Hello,

I've more of 2 exactly 8 file of RNA data that I must import and analyze them with limma. But, I've some problems to import all data within one script. What I done is:

j <- read.delim("1.txt","2.txt","3.txt","4.txt","5.txt","6.txt","7.txt","8.txt", sep = "\t")

Error in match.arg(numerals) : 
  'arg' should be one of “allow.loss”, “warn.loss”, “no.loss”

Maybe someone can help me. 

Sincerely. 

limma rsubread • 723 views
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Dear Justin,

If you still need to read several txt files at once, I recommend you to read this or this.
Furthermore, if you are new to this please  consider reading at least one workflow on how to  perform downstream analysis.
RNA-seq workflow: gene-level exploratory analysis and differential expression

From reads to genes to pathways:Rsubread and the edgeR

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR

More workflows: https://bioconductor.org/packages/release/BiocViews.html#___GeneExpressionWorkflow
Best
Konstantinos

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@gordon-smyth
Last seen 1 hour ago
WEHI, Melbourne, Australia

read.delim() is designed to read just one text file, not a whole set of files. Did you mean to use edgeR::readDGE() instead?

But, if you're using Rsubread you should never to read in a text file at all. The Rsubread featureCounts() function produces an R object directly. You can save it to disk using save() and restore it using load(). There's no need to write text files or to read them with read.delim().

What documentation or example are you following?

Do you know how to read R help pages? When you get an error, you can type help("read.delim") and it will tell you the arguments that the function expects to get. If you know how to read the help page, it tells you what you need to know, i.e., why the code you tried gives an error.

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