WARNING: It is generally ill-advised to merge BIOM datasets, as OTUs mappings are dependent on upstream clustering and are not equivalent between BIOM files.
Usage
biom_merge(
...,
metadata = NA,
taxonomy = NA,
tree = NULL,
sequences = NA,
id = NA,
comment = NA
)
Arguments
- ...
Any number of rbiom objects (e.g. from
read_biom()
), lists of rbiom objects, or valid arguments to thesrc
parameter ofread_biom()
(for instance file names).- metadata, taxonomy, tree, sequences, id, comment
Replace the corresponding data in the merged rbiom object with these values. Set to
NULL
to not inherit a particular component. The default,NA
, will attempt to create the component based on...
values. The merged phylogenetic tree cannot be inferred.
Value
An rbiom object.
See also
Other biom:
bdply()
Examples
library(rbiom)
b1 <- as_rbiom(hmp50$counts[,1:4])
b2 <- as_rbiom(hmp50$counts[,5:8])
biom <- biom_merge(b1, b2)
print(biom)
#>
#> ══ Merged BIOM ═════════════════════════════════════════════
#>
#> 8 Samples: HMP01, HMP02, HMP03, ..., and HMP08
#> 168 OTUs: Unc53100, PpbAcne6, UncO2012, ...
#> 1 Ranks: .otu
#> 1 Fields: .sample
#> Tree: <absent>
#>
#> ── 1.4k - 4.2k reads/sample ────────────────── 2024-10-24 ──
#>
biom$tree <- hmp50$tree
biom$metadata <- hmp50$metadata
#> Warning: ℹ Ignoring metadata for 42 samples not currently in biom object: "HMP09",
#> "HMP10", "HMP11", "HMP12", "HMP13", "HMP14", "HMP15", "HMP16", "HMP17",
#> "HMP18", "HMP19", "HMP20", "HMP21", "HMP22", "HMP23", "HMP24", "HMP25",
#> "HMP26", …, "HMP49", and "HMP50".
print(biom)
#>
#> ══ Merged BIOM ═════════════════════════════════════════════
#>
#> 8 Samples: HMP01, HMP02, HMP03, ..., and HMP08
#> 168 OTUs: Unc53100, PpbAcne6, UncO2012, ...
#> 1 Ranks: .otu
#> 5 Fields: .sample, Age, BMI, Body Site, and Sex
#> Tree: <present>
#>
#> ── 1.4k - 4.2k reads/sample ────────────────── 2024-10-24 ──
#>