Changing .otu names

[TKMarkCheng]

At the moment there is no convenient option to perform changes on .otus like sample names/metadata

A Work around currently is: biom$counts$dimnames[1] followed by changing biom$taxonomy$.otu in the same way.

[dansmith01]

Recent development versions of rbiom allow assignment to biom$otus, like below:

remotes::install_github("cmmr/rbiom")
biom <- rbiom::hmp50$clone()

# See the current OTU names
head(biom$otus)

# Change the OTU names
biom$otus <- paste0("OTU", seq_len(biom$n_otus))

# See the new OTU names
head(biom$otus)
biom$taxonomy
as.matrix(biom$counts[1:4,1:4])

[markyboy30]

@dansmith01 thank you for the swift response. How about for subsetting by otus? (Or otu levels housed in biom$taxonomy)

thank you so much in advance!

[dansmith01]

To drop otus or taxa, you can assign a new otu abundance matrix to biom$counts.

remotes::install_github("cmmr/rbiom")
library(rbiom)
biom <- hmp50$clone()

# Keep 300 most abundant OTUs
keep <- taxa_means(biom) %>% names() %>% head(300)
biom$counts <- biom$counts[keep,]

# Drop specific OTUs
drop <- c("CnbTube3", "PpbAcne6")
keep <- setdiff(biom$otus, drop)
biom$counts <- biom$counts[keep,]

# Keep only OTUs from a specific Phylum
keep <- biom$taxonomy %>% filter(Phylum == "Firmicutes") %>% pull(.otu)
biom$counts <- biom$counts[keep,]