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microbiome / OMA

Orchestrating Microbiome Analysis
https://microbiome.github.io/OMA
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Hardcoded row selection in Multi-omics Integration chapter #498

Closed artur-sannikov closed 1 week ago

artur-sannikov commented 3 months ago

Currently, the selection of rows for Intermediate Fusion algorithm is hardcoded. A better solution would be to select indices based on FeatureType.

pathways_ind <- which(feature_metadata$featureType == "Pathways")
species_ind <- which(feature_metadata$featureType == "Species")

dataList[[1]] <- t(feature_table[pathways_ind, ])
dataList[[2]] <- t(feature_table[species_ind, ])

It's more robust to changes in the number of rows.

TuomasBorman commented 1 month ago

Would you be able to modify?

antagomir commented 1 week ago

PIng @artur-sannikov - is this something we could handle and close?

artur-sannikov commented 1 week ago

It was fixed on July 29. Commit d85b18720f1f5cfef26b683e188cc21c88ed6046. I close it now.