Question: Error in tximport, unused argument (reader = read_tsv)
gravatar for spr
2.0 years ago by
spr0 wrote:


I tried to re-run the same script on the same samples and I encountered this error. 

txi.rsem <- tximport(files, type = "rsem", reader = read_tsv)

Error in tximport(files, type = "rsem", reader = read_tsv) : 

  unused argument (reader = read_tsv)

The only thing that changed between the first time I ran it and this one is I downloaded the latest versions of R and RStudio. 

I tried importing with read.delim instead, but I got the same error.

> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods 
[9] base     

other attached packages:
[1] DESeq2_1.16.1              SummarizedExperiment_1.6.4 DelayedArray_0.2.7       
[4] matrixStats_0.52.2         Biobase_2.36.2             GenomicRanges_1.28.5     
[7] GenomeInfoDb_1.12.2        IRanges_2.10.3             S4Vectors_0.14.4         
[10] BiocGenerics_0.22.0        readr_1.1.1                tximport_1.4.0           
[13] BiocInstaller_1.26.1       refGenome_1.7.3            RSQLite_2.0              
[16] doBy_4.5-15               

loaded via a namespace (and not attached):
[1] locfit_1.5-9.1          Rcpp_0.12.12            lattice_0.20-35       
[4] digest_0.6.12           R6_2.2.2                plyr_1.8.4            
[7] backports_1.1.0         acepack_1.4.1           ggplot2_2.2.1         
[10] zlibbioc_1.22.0         rlang_0.1.2             lazyeval_0.2.0        
[13] data.table_1.10.4       annotate_1.54.0         blob_1.1.0            
[16] rpart_4.1-11            Matrix_1.2-10           checkmate_1.8.3       
[19] splines_3.4.1           BiocParallel_1.10.1     geneplotter_1.54.0    
[22] stringr_1.2.0           foreign_0.8-69          htmlwidgets_0.9       
[25] RCurl_1.95-4.8          bit_1.1-12              munsell_0.4.3         
[28] compiler_3.4.1          base64enc_0.1-3         htmltools_0.3.6       
[31] nnet_7.3-12             tibble_1.3.4            gridExtra_2.3         
[34] htmlTable_1.9           GenomeInfoDbData_0.99.0 Hmisc_4.0-3           
[37] XML_3.98-1.9            MASS_7.3-47             bitops_1.0-6          
[40] grid_3.4.1              xtable_1.8-2            gtable_0.2.0          
[43] DBI_0.7                 magrittr_1.5            scales_0.5.0          
[46] stringi_1.1.5           XVector_0.16.0          genefilter_1.58.1     
[49] latticeExtra_0.6-28     Formula_1.2-2           RColorBrewer_1.1-2    
[52] tools_3.4.1             bit64_0.9-7             hms_0.3               
[55] survival_2.41-3         AnnotationDbi_1.38.2    colorspace_1.3-2      
[58] cluster_2.0.6           memoise_1.1.0           knitr_1.17 
deseq2 tximport • 442 views
ADD COMMENTlink modified 2.0 years ago by Michael Love25k • written 2.0 years ago by spr0

did you try it without the parameter?

ADD REPLYlink written 2.0 years ago by Assa Yeroslaviz1.4k

It seems like reader argument has been replaced with importer. This works just fine:

txi.rsem <- tximport(files, type = "rsem", importer = read_tsv)
ADD REPLYlink written 2.0 years ago by spr0

You can just leave the argument out altogether. Use of readr is default unless the package isn't installed.

ADD REPLYlink written 2.0 years ago by Michael Love25k
Answer: Error in tximport, unused argument (reader = read_tsv)
gravatar for Michael Love
2.0 years ago by
Michael Love25k
United States
Michael Love25k wrote:

You can just leave out the argument. This change is described in NEWS.

ADD COMMENTlink written 2.0 years ago by Michael Love25k
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