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Merge a list_phyloseq into a single phyloseq object

Source: R/merge_lpq.R
merge_lpq.Rd

lifecycle-experimental

Merges all phyloseq objects from a list_phyloseq into a single phyloseq object where each original phyloseq becomes one sample. Abundances are summed across samples within each phyloseq object.

Taxa are matched across phyloseq objects either by reference sequences (refseq slot, default) or by taxa names. Matching by refseq is preferred because taxa names are often inconsistent across independently built phyloseq objects (e.g., ASV_1 in one object is not the same taxon as ASV_1 in another).

Usage

merge_lpq(
  x,
  match_by = c("refseq", "names"),
  tax_priority = 1L,
  verbose = TRUE
)

Arguments

x

(list_phyloseq, required) A list_phyloseq object.

match_by

(character, default "refseq") How to match taxa across phyloseq objects. One of:

  • "refseq": match by DNA sequence in the refseq slot (recommended). All phyloseq objects must have a refseq slot.

  • "names": match by taxa names. Use only when taxa names are consistent across objects (e.g., same pipeline, same database).

tax_priority

(character or integer, default 1L) Which phyloseq object's taxonomy to use when taxa are matched. Either a name from the list or an integer index. When a taxon appears in multiple objects, the taxonomy from the priority object is used; if absent there, the first available taxonomy is used.

verbose

(logical, default TRUE) Print information about the merge.

Value

A phyloseq object with:

otu_table

One column per original phyloseq object (summed across its samples), one row per unique taxon.

sample_data

One row per original phyloseq, with a column source_name containing the list_phyloseq names.

tax_table

Taxonomy from the priority object (or first available).

refseq

Present when match_by = "refseq".

See also

list_phyloseq, simple_venn_pq()

Author

Adrien Taudière

Examples

lpq <- list_phyloseq(list(
  fungi = data_fungi_mini,
  fungi2 = data_fungi_mini
))
#> ℹ Building summary table for 2 phyloseq objects...
#> ℹ Computing comparison characteristics...
#> ℹ Checking sample and taxa overlap...
#> ℹ Detected comparison type: REPRODUCIBILITY
#> ℹ 137 common samples, 45 common taxa
#> ✔ list_phyloseq created (REPRODUCIBILITY)

# Merge by refseq (default)
merged <- merge_lpq(lpq)
#> Merging 2 phyloseq objects by refseq: 45 + 45 taxa -> 45 unique sequences.
merged
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 45 taxa and 2 samples ]
#> sample_data() Sample Data:       [ 2 samples by 2 sample variables ]
#> tax_table()   Taxonomy Table:    [ 45 taxa by 12 taxonomic ranks ]
#> refseq()      DNAStringSet:      [ 45 reference sequences ]

# Merge by taxa names
merged_names <- merge_lpq(lpq, match_by = "names")
#> Merging 2 phyloseq objects by names: 45 + 45 taxa -> 45 unique names.