error with fitTimeSeries in metagenomeSeq" invalid 'times’ argument"
1
0
Entering edit mode
@songeric1107-6996
Last seen 2.8 years ago
United States

I am trying to use the function of fitTimeSeries of metagenomeSeq package.  my dataset are longitudinal dataset of patients. There are multiple data points for each patient

 

If I use fitTimeSeries to one particular genus, it works. e.g.

res = fitTimeSeries(obj=obj,feature="k__Bacteria:p__Firmicutes:c__Clostridia:o__Clostridiales:f__Lachnospiraceae:g__Dorea",class="type",id="patient",time="ime",B=10)

However, when I try to apply to other genera. it failed with error " invalid 'times’ argument"

timeSeriesFits = lapply(classes,function(i){
        fitTimeSeries(obj=obj,
          feature=i,
            class="type",
            id="patient",
            time="time",
            B=100) 
    })

Could anyone give a hint?

microbiome • 792 views
ADD COMMENT
0
Entering edit mode
@joseph-nathaniel-paulson-6442
Last seen 4.3 years ago
United States

Looking at your particular data, the issue is that you can not have the same ID for samples belonging to both classes. You would have to create a separate ID for the ones in one class and ones for the other class or choose one class for the samples.

 

Thank you,

ADD COMMENT

Login before adding your answer.

Traffic: 321 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6