SQM_to_phyloseq: Convert a SQM object into a phyloseq object from the...

In SQMtools: Analyze Results Generated by the 'SqueezeMeta' Pipeline

Convert a SQM object into a phyloseq object from the phyloseq package

Description

This function will convert the selected features from a SQM object into a phyloseq object from the phyloseq package. When possible, it will also include the taxonomy of the included features (for functional classifications, the taxonomy table will instead include the description of each feature ID). Optionally, it accepts a meta table that will be passed as provided to the phyloseq object constructor.

Usage

SQM_to_phyloseq(
  SQM,
  features = "genus",
  count = "abund",
  md = NULL,
  nocds = "treat_separately",
  no_partial_classifications = FALSE,
  ignore_unclassified = FALSE,
  ignore_unmapped = FALSE,
  bin_tax_source = "SQM",
  include_seqs = FALSE
)

Arguments

SQM	A SQM, SQMbunch or SQMlite object.
features	character. Either "orfs", "contigs", "bins", any taxonomic rank included in SQM$taxa or any functional classication included in SQM$functions (default "tax"). Note that a given feature type might not be available in this objects (e.g. "contigs" in SQMlite objects originating from a SQM reads project).
count	character. Either "abund" for raw abundances, "percent" for percentages, "bases" for raw base counts, "cov" for coverages, "cpm" for coverages per million reads, "tpm" for TPM normalized values or "copy_number" for copy numbers (default "abund"). Note that a given count type might not available in this object (e.g. TPM or copy number in SQMlite objects originating from a SQM reads project).
md	data.frame. A optional data.frame containing metadata for the samples in the SQM object.
nocds	character. Either "treat_separately" to treat features annotated as No CDS separately, "treat_as_unclassified" to treat them as Unclassified or "ignore" to ignore them in the output (default "treat_separately").
no_partial_classifications	logical. When features is a taxonomic rank, treat features not fully classified at the requested level (e.g. "Unclassified bacteroidota" at the class level or below) as fully unclassified. This takes effect before ignore_unclassified, so if both are TRUE the plot will only contain features that were fully classified at the requested level (default FALSE).
ignore_unclassified	logical. When features is a taxonomic rank or functional category, don't include unclassified reads in the output (default FALSE).
ignore_unmapped	logical. Don't include unmapped reads in the output (default FALSE).
bin_tax_source	character. Source of taxonomy when features = "bins", either "SQM" of "gtdb" (default "gtdb").
include_seqs	logical. Whether to include sequences or not if creating a microtable from ORFs or contigs (default FALSE).

Value

A phyloseq object.

See Also

SQM_to_microeco for exporting a SQM/SQMlite/SQM object as a microtable object.

SQMtools documentation built on June 8, 2025, 11:16 a.m.