Dear all,
I have a problem concerning sequence retrieval via the getsequence() wrapper function implemented in the biomaRt package. I tried to download a list of sequences based on a list of ensembl transcript IDs. In the example below I included one ID as an example. Regardless of ID lists or single IDs or different sequence types, I always get the error message
Error in martCheck(mart, "ensembl") : This function only works when used with the ensembl BioMart.
My request:
source("http://bioconductor.org/biocLite.R")
biocLite("biomaRt")
library("biomaRt")
Sequences <-getSequence(id = "ENST00000225973", type = "ensembl_transcript_id", seqType = "cdna" , mart = useMart("ENSEMBL_MART_ENSEMBL",dataset = "hsapiens_gene_ensembl", host = "www.ensembl.org"))
In case you wonder why I specified the host: There is an issue with the main biomart portal: Problem with biomart's listMarts function
My sessionInfo():
R version 3.0.0 (2013-04-03) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 LC_PAPER=C [8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.18.0 loaded via a namespace (and not attached): [1] RCurl_1.95-4.1 tools_3.0.0 XML_3.98-1.1
It seems the problem also occurs with the getGene() wrapper (Error: This function only works when used with the ensembl BioMart.) and I have absolutely no clue what the underlying causes could be. So any ideas to bypass this problem are much appreciated!
Thanks for your thoughts!
Best regards,
Robin
Thanks a lot for the information! With using this R/bioconductor version I tried to avoid package unavailability for more recent R versions. I'd really like to use 3.2.4 (or even 3.2.5) but as I'm working on an research institute's cluster without root permissions I'm doomed to take what they got (most recent version R-3.1.2). I'll address this point of this not-up-to-dateness.
Depending on the amount of space they allot you in your home dir (or some other space to which you have write access), you may not be doomed at all. Most linux boxes will compile R without any fuss whatsoever, so you can just download the latest version from here, put it somewhere and then follow these instructions.
Note the line "Note: you do not need to install R: you can run it from where it was built.", which simply means you can add the dir containing the R binary to your path and use it from there. So if you use bash, and install R in your home dir, in say
then you can add
to your .bashrc file, and then when you start R you will use your own personal updated version rather than that ancient version the sysadmin has installed.