Question: tximport all(file.exists(files)) is not TRUE
0
gravatar for ctl
3.0 years ago by
ctl0
London/United Kingdom
ctl0 wrote:

I'm posting this error here to have a clearer idea of what's going on. 

I'm running tximport using my own dataset and following and modifying the instructions on the vignette. But I have found an issue and I can't get around it.

 

I have specified my working directory under the variable dir as follows:

dir <- '/Users/ctl/data/samples/experiment/salmon'

and I have created my files as follows:

files <- file.path(dir, samples$run, "quant.genes.sf")

which gives me an output like this:

"/Users/ctl/data/samples/experiment/salmon/run_1/quant.genes.sf"

Now, if I add the sample name as follows:

names(files) <- paste0(samples$run)

I get this:

                                                                                               run_1

"/Users/ctl/data/samples/experiment/salmon/run_1/quant.genes.sf"

                                                                                               run_2

"/Users/ctl/data/samples/experiment/salmon/run_2/quant.genes.sf"

 

And this result agrees with what I have in that directory and inside each sample folder. However, when I check if all files are listed, I get this error:

all(file.exists(files))

FALSE

In my previous (misplaced) post on GitHub issues, I was told that I am not providing the right directory for the files, but it seem I am providing it correctly. Any hints to how can I solve this problem?

 

Thanks in advance!

 

 

rnaseq R bioconductor tximport • 3.0k views
ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by ctl0

facing the same issue.input is like this

gene id TPM
avd 4
bvn 5

code used

library("tximport")
a<-read.table("tpm_sorghum.csv",header=TRUE)
typeof(a)
txi<-as.matrix(a)
typeof(txi)
head(txi)
DESeq2_output<-tximport(txi)

after this portion the error creep in.can anyone help me????

ADD REPLYlink written 15 months ago by akhilkrishnavs0

 As I said in the other reply this means the files don’t exist at the location specified. 

ADD REPLYlink written 15 months ago by Michael Love25k
Answer: tximport all(file.exists(files)) is not TRUE
0
gravatar for Michael Love
3.0 years ago by
Michael Love25k
United States
Michael Love25k wrote:

You can try:

file.exists(files)

To see if all or just some are not present at the location you specified. 

If they are all not present, make sure you have specified the path correctly. You can work backwards, e.g.:

file.exists("/Users/ctl/data/samples/experiment/salmon")

file.exists("/Users/ctl/data/samples/experiment")

...
ADD COMMENTlink written 3.0 years ago by Michael Love25k
Answer: tximport all(file.exists(files)) is not TRUE
0
gravatar for ctl
3.0 years ago by
ctl0
London/United Kingdom
ctl0 wrote:

Hi!

Yes, that helped me to solve the problem. There was an issue with my sample file. 

Thanks a lot for the support. 

ADD COMMENTlink written 3.0 years ago by ctl0
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