Hello,

I am really sorry if it's not the kind of question I should be asking here but I did not find any help at BioStars forum, so...

I am trying to incorporate my "taxonomy table" from metagenomic reads data into Tree/SummarizedExperiment and have found no luck. The tutorials/workflow I have seen are using "Global Patterns" dataset which does not require importing rowLinks, rowTree data manually.

My code:

counts <- read.csv("counts_file.csv", header = T)
pdata <- read_csv("coldata_file.csv")
taxa <- read.csv("taxa_file.csv")    
pdata <- column_to_rownames(pdata, "sample_id")    
counts <- column_to_rownames(counts, "species")    
se <- SummarizedExperiment(t(counts), colData = pdata, rowData = taxa)    
se
tse <- as(se, "TreeSummarizedExperiment")
tse

this is how my tse looks like:

class: TreeSummarizedExperiment 
dim: 3107 27 
metadata(0):
assays(1): ''
rownames(3107): X.Candida._auris X.Candida._duobushaemulonis ... Zymomonas_mobilis
  Zymoseptoria_tritici
rowData names(7): domain phylum ... genus species
colnames(27): control_2 ILVO650SCE ... ILVO747CE winter78Healthy
colData names(3): health_status group sample_location
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):
rowLinks: NULL
rowTree: NULL
colLinks: NULL
colTree: NULL

I know I cannot just make tse with as function but I have not found an alternative way to fix this.

Thanks for your help.

Does the vignette not help?