subsetBins: Create a SQM object containing only the requested bins, and...

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

Create a SQM object containing only the requested bins, and the contigs and ORFs contained in them.

Description

Create a SQM object containing only the requested bins, and the contigs and ORFs contained in them.

Usage

subsetBins(
  SQM,
  bins = NULL,
  rank = NULL,
  tax = NULL,
  min_completeness = NULL,
  max_contamination = NULL,
  tax_source = "bins",
  trusted_functions_only = FALSE,
  ignore_unclassified_functions = FALSE,
  rescale_tpm = TRUE,
  rescale_copy_number = TRUE,
  allow_empty = FALSE
)

Arguments

SQM	SQM object to be subsetted.
bins	character. Vector of bins to be selected. If provided, will override rank, tax, min_completeness and max_contamination.
rank	character. The taxonomic rank from which to select the desired taxa (superkingdom, phylum, class, order, family, genus, species)
tax	character. A taxon or vector of taxa to be selected.
min_completeness	numeric. Discard bins with completeness lower than this value (default NULL).
max_contamination	numeric. Discard bins with contamination higher than this value (default NULL).
tax_source	character, source data used for taxonomic subsetting (if rank and tax are provided) and for the aggregate taxonomy tables present in SQM$taxa, either "orfs", "contigs", "bins" (GTDB bin taxonomy if available, SQM bin taxonomy otherwise), "bins_gtdb" (GTDB bin taxonomy) or "bins_sqm" (SQM bin taxonomy). If using bins_gtdb, note that GTDB taxonomy may differ from the NCBI taxonomy used throughout the rest of SqueezeMeta. Default "bins".
trusted_functions_only	logical. If TRUE, only highly trusted functional annotations (best hit + best average) will be considered when generating aggregated function tables. If FALSE, best hit annotations will be used (default FALSE).
ignore_unclassified_functions	logical. If FALSE, ORFs with no functional classification will be aggregated together into an "Unclassified" category. If TRUE, they will be ignored (default FALSE).
rescale_tpm	logical. If TRUE, TPMs for KEGGs, COGs, and PFAMs will be recalculated (so that the TPMs in the subset actually add up to 1 million). Otherwise, per-function TPMs will be calculated by aggregating the TPMs of the ORFs annotated with that function, and will thus keep the scaling present in the parent object. By default it is set to TRUE, which means that the returned TPMs will be scaled by million of reads of the selected bins.
rescale_copy_number	logical. If TRUE, copy numbers with be recalculated using the median single-copy gene coverages in the subset. Otherwise, single-copy gene coverages will be taken from the parent object. By default it is set to TRUE, which means that the returned copy numbers for each function will represent the average copy number of that function per genome of the selected taxon.
allow_empty	(internal use only).

Value

SQM object containing only the requested bins.

See Also

subsetContigs, subsetORFs

Examples

data(Hadza)
# Which are the most complete bins?
topBinNames = rownames(Hadza$bins$table)[order(Hadza$bins$table[,"Completeness"],
                                         decreasing=TRUE)][1:2]
# Subset with the most complete bin.
topBin = subsetBins(Hadza, topBinNames[1])

# Subset with all the bins over 90% completeness
over90 = subsetBins(Hadza, min_completeness = 90)

# Subset with bins from the Phascolarctobacterium genus using SqueezeMeta's taxonomy
phasco = subsetBins(Hadza, tax_source = "bins_sqm", rank = "genus", tax = "Phascolarctobacterium")

# Subset with binsfrom the Bacteroidota phylum using GTDB taxonomy
bact = subsetBins(Hadza, tax_source = "bins_gtdb", rank = "phylum", tax = "Bacteroidota")

SQMtools documentation built on Aug. 27, 2026, 9:07 a.m.