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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 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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)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.
Thank you very much
it worked now, after installing newer version