How do you set factors in the mStat object?

[RachBioHaz]

Hi, I imported a phyloseq object using mStat_convert_phyloseq_to_data_obj. I lost the factors I had in the phyloseq object. How do I set up factors in the order I need in the new MicrobiomeStat object?
Thanks

[cafferychen777]

Hi @RachBioHaz ,

Thank you for reaching out. It seems that you want to retain or set up factors in a specific order in the MicrobiomeStat object after importing from a phyloseq object. Here's how you can achieve this:

1. After converting your phyloseq object to a MicrobiomeStat object using mStat_convert_phyloseq_to_data_obj, you'll get an object similar to peerj32.obj.
2. To set up factors in the order you need, you can use the following code:

# Assuming 'sex' is the metadata column you want to set as a factor in a specific order
peerj32.obj$meta.dat$sex <- factor(as.factor(peerj32.obj$meta.dat$sex), levels = c("male", "female"))

3. To check the order and the data:

print(peerj32.obj$meta.dat$sex)

The output will display the data in the specified factor order.

Remember to replace 'sex' with the actual metadata column name you're interested in, and c("male", "female") with the desired order of your factor levels.

I hope this helps. Let me know if you have any further questions!

Best regards,
Chen YANG

[RachBioHaz]

Thanks