I used kraken to get the taxonomic abbundance estimations for my shotgun data. The output I get from kraken contains both counts and taxonomy. This format is however not supported to set up an MRexperiment object for that I would need an OTU table and a taxonomy table. As a workaround I created a biom-file with kraken and was able to set up a MRexperiment object with the biom2MRexperiment function. Both however, the biom-file and MRexperiment object do not contain any phenotypic information. I would like to use the fitTimeSeries function to analyze my data but to do this I need the PhenoData information in my MRexperiment object. I there any chance to extend the MRexperiment object with phenoData or do you have another solution for me?
Hey,
I used kraken to get the taxonomic abbundance estimations for my shotgun data. The output I get from kraken contains both counts and taxonomy. This format is however not supported to set up an MRexperiment object for that I would need an OTU table and a taxonomy table. As a workaround I created a biom-file with kraken and was able to set up a MRexperiment object with the biom2MRexperiment function. Both however, the biom-file and MRexperiment object do not contain any phenotypic information. I would like to use the fitTimeSeries function to analyze my data but to do this I need the PhenoData information in my MRexperiment object. I there any chance to extend the MRexperiment object with phenoData or do you have another solution for me?
Thank you in advance!