Question: unable to load quant.sf files
0
gravatar for shivyasoni1994
7 weeks ago by
shivyasoni19940 wrote:

Hi, I am am trying to use tximport, but running into:

all(file.exists(files))
[1] FALSE

I started like this:

I imported the libraries

library("tximport")

then

library("readr")

I refered to directory, containig the quant.sf files

dir <- '/home/dell/Desktop/quant'

inside directory quant

> list.files(dir)

[1] "gencode.v28.annotation.sqlite" "quant3.sf"                    
[3] "quant4.sf"                     "quant5.sf"                    
[5] "quant6.sf"                     "quant7.sf"                    
[7] "sample.txt"

then, sample.txt file

> samples <- read.table(file.path(dir, "sample.txt"), header = TRUE)

veiw of sample.txt

> samples

  run_id condition
1 quant3  NormalF5
2 quanr4  NormalM7
3 quant5   TumorM7
4 quant6   TumorF6

tried this

> files <- c("'/home/dell/Desktop/quant/quant3.sf'","'/home/dell/Desktop/quant/quant4.sf'","'/home/dell/Desktop/quant/quant5.sf'","'/home/dell/Desktop/quant/quant6.sf'")

then

> names(files) <- paste0("run_id", 1:4)

and got

> all(file.exists(files))
[1] FALSE

Kindly suggest possible solution. Thanks in advance

R tximport • 192 views
ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by shivyasoni19940

Hello shivyasoni1994 ,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

Thank you!

ADD REPLYlink written 7 weeks ago by finswimmer7.7k

Thankyou ......................!

ADD REPLYlink written 7 weeks ago by shivyasoni19940
3
gravatar for rizoic
7 weeks ago by
rizoic190
rizoic190 wrote:

Can you add the output when you enter files on the terminal. You should not have both double/single quotes when you initialize files. Try removing the single quotes and changing the statement where you initialize files to files <- c("/home/dell/Desktop/quant/quant3.sf", {same for other files}).

ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by rizoic190

Thankyou so much, it solved my problem.. thankyou!!!!

ADD REPLYlink written 7 weeks ago by shivyasoni19940
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