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DaliangNing / iCAMP1

Infer Community Assembly Mechanisms by Phylogenetic bin-based null model analysis (Version 1)
GNU General Public License v2.0
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Failing to match OTU IDs #1

Closed nejcstopno closed 3 years ago

nejcstopno commented 3 years ago

Hi Daliang, While running iCAMP pipeline (icamp.test.r) on my own dataset it is failing to match OTU IDs (Step #5). However, I am not sure why this issue comes up since all tree tip labels match the OTU names in the count and taxonomy tables.

> summary(tree$tip.label %in% colnames(comm))
  Mode    TRUE 
logical   22003

> summary(tree$tip.label %in% (clas$SpeciesID))
   Mode    TRUE 
logical   22003

Any suggestions on what to change?

I generated the nwk tree in QIIME2, imported it into R and done some filtering using phyloseq. I exported the final tree using the phy_tree() function from the phyloseq package and saved it as .nwk with write.tree() function from the ape package.

DaliangNing commented 3 years ago

You may send me (ningdaliang@ou.edu) the files and your code for a test : )