Question: Error in tximport, unused argument (reader = read_tsv)
0
gravatar for spr
21 months ago by
spr0
spr0 wrote:

Hello,

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

locale:
[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 • 385 views
ADD COMMENTlink modified 21 months ago by Michael Love24k • written 21 months ago by spr0
1

did you try it without the parameter?

ADD REPLYlink written 21 months 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 21 months 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 21 months ago by Michael Love24k
Answer: Error in tximport, unused argument (reader = read_tsv)
1
gravatar for Michael Love
21 months ago by
Michael Love24k
United States
Michael Love24k wrote:

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

ADD COMMENTlink written 21 months ago by Michael Love24k
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