Problem with BiomaRt::useMart function Landscape Genomics
1
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Entering edit mode
6 months ago

Hello everyone,

the problem I would like to solve is not easy to explain but I will try to explain it as best I can. I'm workin with the R.SamBada package for Landscape Genomics analyis, and I'm running into a problem. When I use the 'plotResultInteractive' function, which is used to interactively display the manhattan plot for the associations between SNP and clinical variables, I cannot finish the job because this happens:

plotResultInteractive(preparedOutput = prep, varEnv = 'cb3', envFile = envFile2, x='longitude', y='latitude', gdsFile = gdsFile, IDCol = 'acc_id', species = 'athaliana', pass = 25000)
Error in ensembl_connection(species, ensemblHost, TRUE) : 
  Species not found in ensembl database. Either change the name of the species (latin naming e.g. btaurus for cattle) or set it to NULL

The problem is that the 'ensmbleHost' argument looks in the ensembl dataset dedicated to animals, but I need the one of plants, as I work with Arabidopsis. The package refers to this function

 biomaRt::useMart
function (biomart, dataset, host = "https://www.ensembl.org", 
    path = "/biomart/martservice", port, archive = FALSE, ensemblRedirect = NULL, 
    version, verbose = FALSE) 
{
    if (missing(port)) {
        port <- ifelse(grepl("https", host), yes = 443, no = 80)
    }
    if (!is.null(ensemblRedirect)) {
        warning("The argument \"ensemblRedirect\" has been deprecated and will be removed in the next biomaRt release.")
    }
    mart <- .useMart(biomart, dataset, host = host, path = path, 
        port = port, archive = archive, version = version, verbose = verbose, 
        ensemblRedirect = TRUE)
}
<bytecode: 0x55e1bffcbb18="">
<environment: namespace:biomaRt="">

How can I change this function so that the package looks in the 'plant.ensembl.org' dataset?

I hope I was clear

Thanks to everyone that can give me an hand with this.

Simone

landcape genomics BiomaRt usaMart ensembl plant • 263 views
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Entering edit mode
6 months ago

host = "https://plants.ensembl.org"

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