8000 Improve import: ensure that rownames of metadata are identical to colnames of TreeSE by artur-sannikov · Pull Request #691 · microbiome/OMA · GitHub
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Improve import: ensure that rownames of metadata are identical to colnames of TreeSE #691

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Improve import: ensure that rownames of metadata are identical to colnames of TreeSE #691

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artur-sannikov
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TuomasBorman
TuomasBorman requested changes Mar 19, 2025
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Thanks!

This checks different thing than we talked

See this:

library(TreeSummarizedExperiment)

tse <- makeTSE()
mat <- assay(tse)
cd <- colData(tse)
# Mess up sample names
rownames(cd) <- paste0("sample_name_", seq_len(nrow(cd)))

# Fails
tse_taxa <- TreeSummarizedExperiment(
    assays =  SimpleList(counts = mat),
    colData = cd
)

# If colData is replaced, names are overwritten
colnames(tse)
colData(tse) <- cd
colnames(tse)

Constructor checks every time that the sample names match. Your mistake happened when you overwrote the existing colData() with new one (SE does not check that sample names match in that case).

Can you update this accordingly?

@TuomasBorman
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Any updates on this? @artur-sannikov

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Discussed with @artur-sannikov and we decided to implement the example differently: #703

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