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> slices=c(0:0.5)
> Betas=BDTT(similarity_slices=slices,tree=tree,sampleOTUs=amt)
[1] "0 similarity provides 142906 total new OTUs"
Error in .M.kind(data) :
not yet implemented for matrix with typeof character
some notes: my tree was in newick format (I imported it with ape so not sure if I need to use something different) and I have modified the OTUIDs like so:
where the taxonomy levels are separated by a '|' and the OTUID is appended at the end. My tree tips are also labeled like this.
Any pointers on what the error could be? Can attach files if needed as well.
EDIT/UPDATE:
I realized I may need to have turned the otu table into a proper matrix. So I went ahead did that but also made a small test dataset with 3 samples to make sure it wasn't a large dataset issue. Now I get this error:
Error in onlyBeta == F :
comparison (1) is possible only for atomic and list types
#Here is my code:
ttree=phytools::read.newick('amttree.nwk')
tamt=read.table('amtesttable.tsv',sep="\t",header=TRUE,row.names=1)
tamtm=as.matrix(tamt)
head(tamt)
slices=c(0:0.5)
Betas=BDTT(similarity_slices=slices,tree=ttree,sampleOTUs=tamt)
Error in onlyBeta == F :
comparison (1) is possible only for atomic and list types
Also attached a pic of my otu table.
The text was updated successfully, but these errors were encountered:
Hi all,
When I attempt to run BDTT I get this outcome:
some notes: my tree was in newick format (I imported it with ape so not sure if I need to use something different) and I have modified the OTUIDs like so:
d__Bacteria; p__Bacteroidota; c__Bacteroidia; o__Bacteroidales; f__Bacteroidales_RF16_group; g__Bacteroidales_RF16_group; s__uncultured_bacterium|00009c1cc42953fb4702f6331325c7cc
where the taxonomy levels are separated by a '|' and the OTUID is appended at the end. My tree tips are also labeled like this.
Any pointers on what the error could be? Can attach files if needed as well.
EDIT/UPDATE:
I realized I may need to have turned the otu table into a proper matrix. So I went ahead did that but also made a small test dataset with 3 samples to make sure it wasn't a large dataset issue. Now I get this error:
Also attached a pic of my otu table.
The text was updated successfully, but these errors were encountered: