Question: error with fitTimeSeries in metagenomeSeq" invalid 'times’ argument"
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gravatar for songeric1107
5.0 years ago by
United States
songeric11070 wrote:

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 • 688 views
ADD COMMENTlink modified 5.0 years ago by Joseph Nathaniel Paulson270 • written 5.0 years ago by songeric11070
Answer: error with fitTimeSeries in metagenomeSeq" invalid 'times’ argument"
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gravatar for Joseph Nathaniel Paulson
5.0 years ago by
United States
Joseph Nathaniel Paulson270 wrote:

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 COMMENTlink written 5.0 years ago by Joseph Nathaniel Paulson270
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