Question: tximport and its version
0
gravatar for Mithil Gaikwad
6 months ago by
Tezpur University, India
Mithil Gaikwad0 wrote:

Hello, I am usingtximport after StringTie quantification step, but I guess my tximport is not installed properly, because it is not accepting "stringtie" option and also not the none option:
Is there any way to install tximport newer version or any other way.

txi <- tximport(files, type = "stringtie", tx2gene = tx2gene)
    Error in match.arg(type, c("none", "salmon", "sailfish", "kallisto", "rsem")) :
      'arg' should be one of “none”, “salmon”, “sailfish”, “kallisto”, “rsem”

txi <- tximport(files, type = "none", tx2gene = tx2gene)
reading in files with read_tsv
1 Error in c(lengthCol, abundanceCol) %in% names(raw) :
  argument "lengthCol" is missing, with no default


> session_info()
─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.4.4 (2018-03-15)
 os       Ubuntu 18.04.1 LTS          
 system   x86_64, linux-gnu           
 ui       RStudio                     
 language en_IN:en                    
 collate  en_IN.UTF-8                 
 ctype    en_IN.UTF-8                 
 tz       Asia/Kolkata                
 date     2018-11-19                  

─ Packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package              * version   date       lib source        
 acepack                1.4.1     2016-10-29 [1] CRAN (R 3.4.4)
 annotate               1.56.2    2018-11-08 [1] Bioconductor  
 AnnotationDbi          1.40.0    2018-11-08 [1] Bioconductor  
 assertthat             0.2.0     2017-04-11 [1] CRAN (R 3.4.4)
 backports              1.1.2     2017-12-13 [1] CRAN (R 3.4.4)
 base64enc              0.1-3     2015-07-28 [1] CRAN (R 3.4.4)
 bindr                  0.1.1     2018-03-13 [1] CRAN (R 3.4.4)
 bindrcpp               0.2.2     2018-03-29 [1] CRAN (R 3.4.4)
 Biobase              * 2.38.0    2018-10-25 [1] Bioconductor  
 BiocGenerics         * 0.24.0    2018-10-25 [1] Bioconductor  
 BiocParallel           1.12.0    2018-11-07 [1] Bioconductor  
 bit                    1.1-14    2018-05-29 [1] CRAN (R 3.4.4)
 bit64                  0.9-7     2017-05-08 [1] CRAN (R 3.4.4)
 bitops                 1.0-6     2013-08-17 [1] CRAN (R 3.4.4)
 blob                   1.1.1     2018-03-25 [1] CRAN (R 3.4.4)
 callr                  3.0.0     2018-08-24 [1] CRAN (R 3.4.4)
 checkmate              1.8.5     2017-10-24 [1] CRAN (R 3.4.4)
 cli                    1.0.1     2018-09-25 [1] CRAN (R 3.4.4)
 cluster                2.0.6     2017-03-16 [4] CRAN (R 3.4.2)
 colorspace             1.3-2     2016-12-14 [1] CRAN (R 3.4.4)
 crayon                 1.3.4     2017-09-16 [1] CRAN (R 3.4.4)
 curl                   3.2       2018-03-28 [1] CRAN (R 3.4.4)
 data.table             1.11.8    2018-09-30 [1] CRAN (R 3.4.4)
 DBI                    1.0.0     2018-05-02 [1] CRAN (R 3.4.4)
 DelayedArray         * 0.4.1     2018-11-07 [1] Bioconductor  
 desc                   1.2.0     2018-05-01 [1] CRAN (R 3.4.4)
 DESeq2               * 1.18.1    2018-11-08 [1] Bioconductor  
 devtools             * 2.0.1     2018-10-26 [1] CRAN (R 3.4.4)
 digest                 0.6.18    2018-10-10 [1] CRAN (R 3.4.4)
 dplyr                  0.7.8     2018-11-10 [1] CRAN (R 3.4.4)
 foreign                0.8-69    2017-06-21 [4] CRAN (R 3.4.2)
 Formula                1.2-3     2018-05-03 [1] CRAN (R 3.4.4)
 fs                     1.2.6     2018-08-23 [1] CRAN (R 3.4.4)
 genefilter             1.60.0    2018-11-08 [1] Bioconductor  
 geneplotter            1.56.0    2018-11-08 [1] Bioconductor  
 GenomeInfoDb         * 1.14.0    2018-11-07 [1] Bioconductor  
 GenomeInfoDbData       1.0.0     2018-10-25 [1] Bioconductor  
 GenomicRanges        * 1.30.3    2018-11-07 [1] Bioconductor  
 ggplot2                3.1.0     2018-10-25 [1] CRAN (R 3.4.4)
 glue                   1.3.0     2018-07-17 [1] CRAN (R 3.4.4)
 gridExtra              2.3       2017-09-09 [1] CRAN (R 3.4.4)
 gtable                 0.2.0     2016-02-26 [1] CRAN (R 3.4.4)
 Hmisc                  4.1-1     2018-01-03 [1] CRAN (R 3.4.4)
 hms                    0.4.2     2018-03-10 [1] CRAN (R 3.4.4)
 htmlTable              1.12      2018-05-26 [1] CRAN (R 3.4.4)
 htmltools              0.3.6     2017-04-28 [1] CRAN (R 3.4.4)
 htmlwidgets            1.3       2018-09-30 [1] CRAN (R 3.4.4)
 IRanges              * 2.12.0    2018-10-25 [1] Bioconductor  
 knitr                  1.20      2018-02-20 [1] CRAN (R 3.4.4)
 lattice                0.20-35   2017-03-25 [4] CRAN (R 3.4.2)
 latticeExtra           0.6-28    2016-02-09 [1] CRAN (R 3.4.4)
 lazyeval               0.2.1     2017-10-29 [1] CRAN (R 3.4.4)
 locfit                 1.5-9.1   2013-04-20 [1] CRAN (R 3.4.4)
 magrittr               1.5       2014-11-22 [1] CRAN (R 3.4.4)
 Matrix                 1.2-12    2017-11-16 [4] CRAN (R 3.4.2)
 matrixStats          * 0.54.0    2018-07-23 [1] CRAN (R 3.4.4)
 memoise                1.1.0     2017-04-21 [1] CRAN (R 3.4.4)
 munsell                0.5.0     2018-06-12 [1] CRAN (R 3.4.4)
 nnet                   7.3-12    2016-02-02 [4] CRAN (R 3.4.2)
 pillar                 1.3.0     2018-07-14 [1] CRAN (R 3.4.4)
 pkgbuild               1.0.2     2018-10-16 [1] CRAN (R 3.4.4)
 pkgconfig              2.0.2     2018-08-16 [1] CRAN (R 3.4.4)
 pkgload                1.0.2     2018-10-29 [1] CRAN (R 3.4.4)
 plyr                   1.8.4     2016-06-08 [1] CRAN (R 3.4.4)
 prettyunits            1.0.2     2015-07-13 [1] CRAN (R 3.4.4)
 processx               3.2.0     2018-08-16 [1] CRAN (R 3.4.4)
 ps                     1.2.1     2018-11-06 [1] CRAN (R 3.4.4)
 purrr                  0.2.5     2018-05-29 [1] CRAN (R 3.4.4)
 R6                     2.3.0     2018-10-04 [1] CRAN (R 3.4.4)
 RColorBrewer           1.1-2     2014-12-07 [1] CRAN (R 3.4.4)
 Rcpp                   1.0.0     2018-11-07 [1] CRAN (R 3.4.4)
 RCurl                  1.95-4.11 2018-07-15 [1] CRAN (R 3.4.4)
 readr                * 1.1.1     2017-05-16 [1] CRAN (R 3.4.4)
 remotes                2.0.2     2018-10-30 [1] CRAN (R 3.4.4)
 rlang                  0.3.0.1   2018-10-25 [1] CRAN (R 3.4.4)
 rpart                  4.1-13    2018-02-23 [4] CRAN (R 3.4.3)
 rprojroot              1.3-2     2018-01-03 [1] CRAN (R 3.4.4)
 RSQLite                2.1.1     2018-05-06 [1] CRAN (R 3.4.4)
 rstudioapi             0.8       2018-10-02 [1] CRAN (R 3.4.4)
 S4Vectors            * 0.16.0    2018-10-25 [1] Bioconductor  
 scales                 1.0.0     2018-08-09 [1] CRAN (R 3.4.4)
 sessioninfo            1.1.1     2018-11-05 [1] CRAN (R 3.4.4)
 stringi                1.2.4     2018-07-20 [1] CRAN (R 3.4.4)
 stringr                1.3.1     2018-05-10 [1] CRAN (R 3.4.4)
 SummarizedExperiment * 1.8.1     2018-11-07 [1] Bioconductor  
 survival               2.41-3    2017-04-04 [4] CRAN (R 3.4.2)
 tibble                 1.4.2     2018-01-22 [1] CRAN (R 3.4.4)
 tidyselect             0.2.5     2018-10-11 [1] CRAN (R 3.4.4)
 tximport             * 1.6.0     2018-11-16 [1] Bioconductor  
 usethis              * 1.4.0     2018-08-14 [1] CRAN (R 3.4.4)
 withr                  2.1.2     2018-03-15 [1] CRAN (R 3.4.4)
 XML                    3.98-1.16 2018-08-19 [1] CRAN (R 3.4.4)
 xtable                 1.8-3     2018-08-29 [1] CRAN (R 3.4.4)
 XVector                0.18.0    2018-10-25 [1] Bioconductor  
 zlibbioc               1.24.0    2018-10-25 [1] Bioconductor  

[1] /home/mithil/R/x86_64-pc-linux-gnu-library/3.4
[2] /usr/local/lib/R/site-library
[3] /usr/lib/R/site-library
[4] /usr/lib/R/library
>
ADD COMMENTlink modified 6 months ago by James W. MacDonald50k • written 6 months ago by Mithil Gaikwad0
Answer: tximport and its version
0
gravatar for James W. MacDonald
6 months ago by
United States
James W. MacDonald50k wrote:

From the NEWS file:

 

CHANGES IN VERSION 1.8.0
------------------------

    o Added support for StringTie output.
ADD COMMENTlink written 6 months ago by James W. MacDonald50k

Sorry, I didn't understand

Can you please elaborate, What can I do to update my tools.

 

if (!requireNamespace("BiocManager", quietly = TRUE))
+     install.packages("BiocManager")
Installing package into ‘/home/mithil/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘BiocManager’ is not available (for R version 3.4.4)

 

ADD REPLYlink written 6 months ago by Mithil Gaikwad0

Bioconductor packages are tightly aligned with the version of R you are using. You have R-3.4.4 installed, which is an old version of R, and which will result in old versions of BioC packages being installed. If you want to use the most updated versions of Bioconductor packages (and you should!), you will have to keep current with your version of R. So install R-3.5.2 and then BiocManager, and then whatever packages you want (including tximport), and you should be good to go.

ADD REPLYlink written 6 months ago by James W. MacDonald50k

Thank you very much

it worked now, after installing newer version

 

ADD REPLYlink written 6 months ago by Mithil Gaikwad0
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