Hi QIIME Users,
When will aldex.glm module be included in q2aldex? Until that time, can any one please explain what is the inputs to create a model matrix to use it with aldex.clr in R?
As ALDEx2_vignette states, I need a RangedSummarizedExperiment object and vector containing a descriptor for the samples. I have ASVs table and metadata file for three groups.
My questions are, how can I convert them to dataframe of reads, do I need to merge them?
what are the covariates and mm in the documentation mean? Are they corresponding to the vector of conditions(condos)? Please excuse my shallow knowledge and would appreciate if you provide any tutorial or link can help when working with more than two groups.
@fedarko would you please help on that.
Sorry, I’m not qualified to speak about this. You may find an answer from the maintainer email address listed on ALDEx2’s bioconductor page.
I don’t know enough R to help with this. If you haven’t already I would suggest walking through the GLM example in the ALDEx2 reference manual (see the top of page 13) and observing what the input variables used (
mm) all look like. This should be a good starting point for seeing how your data will eventually need to be formatted. You may also be interested in the awesome qiime2R package, which was designed for loading QIIME 2 outputs like your ASV table in R.
From looking over section 5.6 of the vignette, I think you’re on the right track –
covariates seems to be analogous to an ordinary sample metadata file (loaded as an R
mm is a model matrix (aka a design matrix) that’s created based on an R formula and
Thank you for your help and yes I loaded my data using qiime2R package which is really awesome.