Question

tximport ERROR : all(file.exists(files)) is not TRUE

0

Entering edit mode

nakane_clan • 0

@d82dd0af

Last seen 2.7 years ago

Japan

I am using Fedora35 to study expression level analysis.

I want to load the following file (Sample2condition.txt) with tximport.

enter image description here

So, I executed the command in the directory where the data file is located, using the following procedure.

$ s2c <- read.table("sample2condition.txt", header=T, sep="\t", stringsAsFactors=F)
$ s2c$group <- gsub(" ", "_", s2c$group) 

$ bfiles <- s2c$path
$ names(files) <- s2c$sample

$ txi <- tximport(files, type="rsem", txIn=F, txOut=F)

However, I get an error message saying "all(file.exists(files)) is not TRUE" and cannot proceed.

What is the problem?

Linux R tximport • 2.9k views

ADD COMMENT • link 2.7 years ago nakane_clan • 0

score 0 · Answer 1 · 2022-02-25

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Entering edit mode

Michael Love 43k

@mikelove

Last seen 11 hours ago

United States

This means that the files do not exist at the location you specified.

Some R basics:

getwd() # tells you R's working directory

list.files(".") # tells you what files are in a particular location

Just look at files and work out why the files aren't where you specified.

ADD COMMENT • link 2.7 years ago Michael Love 43k

0

Entering edit mode

Thank you for your answer.

I have tried the method you taught me.

>getwd()
>"/home/expression/STAR"

>list.files(".")
>"sample2condition.txt"

The error does not go away even though the necessary files are in the working directory as shown above.

ADD REPLY • link 2.7 years ago nakane_clan • 0