Uploading input files using the R console

[Juliana-Soto24]

Hi,

I was wondering how can I load the feature count data, phenotype info, and taxonomy info files using the R console and not the GUI or shiny application.
In tutorial, there is only the this option for uploading data:
data("mouseData", package = "metagenomeSeq")
meData <- filterMEData(mouseData,minpresence = 1, minfeats = 2, minreads = 2)

Thanks,

Juliana

[zoecastillo]

Thank you for pointing this out. That is a very good point. I will update the documentation to include this.

There are a few functions in the functions.R file that help with this. You can use "readData" to process an RDS file already storing an MRExperiment or to load a counts matrix stored in tabular format (it has a parameter "type" which you can set according to the type of data). For the latter case, you would then use the functions "addPheno" and "addFeat" to add phenotype data and the taxonomy information.

I hope this helps for now.