RNASeq Salmon tximport error

Question

[Claire]

Hi everyone

I am new to this. I am trying to run do egdeR after Salmon quantification and using tximport to move from transcript level to gene level. My code is:

 names(files) <- paste0("sample", 1:4) 
 print(names)
 file.exists(files)
 tr2gene <- read.csv("tx2gene.csv") 
 txi <- tximport(files, type ="salmon",txIn = TRUE, tx2gene = tr2gene)

I got this error:

Error in tximport(files, type = "salmon", txIn = TRUE, tx2gene = tr2gene) : 
  unused argument (tx2gene = tr2gene)

I tried txOUT = False same error.

I checked tr2gene, it is read correctly and exists. Also checked files:

>     [1] "sample1.s_1.stress.quant.sf"   "sample2.s_1.stress.quant.sf"  
>     [3] "sample3.s_1.wildtype.quant.sf" "sample4.s_1.wildtype.quant.sf"
>     function (x)  .Primitive("names")
>     [1] TRUE TRUE TRUE TRUE

Thank you

[i.sudbery]

What version of tximport are you using? What is the output of sessionInfo()

[Claire]

tximport version is 0.0.15
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.9 (Nitrogen)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] tximport_0.0.15

Thank you

[i.sudbery]

This is a very, very old version of tximport. It probably doesn't work the same way as the manual suggests it does. Try updating to a more recent version.

[Claire]

Ok thanks so much. Will try this out.

[Claire]

Just in case someone comes through this error, upgrading tximport fixed it. Thank you i.sudbery !