combineSQM: Combine several SQM objects
In SQMtools: Analyze Results Generated by the 'SqueezeMeta' Pipeline

combineSQM

R Documentation

Combine several SQM objects

Description

Combine an arbitrary number of SQM objects into a single SQM object (if the input objects contain the same samples, i.e. they come from the same SqueezeMeta run) or a single SQMbunch object. For combining results from sqm_reads.pl or sqm_longreads.pl please check combineSQMlite. The parameters below (other than ...) will take only effect if the input objects contain the same samples. Otherwise the input objects will be taken as they are, with no recalculation of taxonomy, function or rescaling,

Usage

combineSQM(
  ...,
  tax_source = "orfs",
  trusted_functions_only = FALSE,
  ignore_unclassified_functions = FALSE,
  rescale_tpm = TRUE,
  rescale_copy_number = TRUE,
  recalculate_bin_stats = TRUE
)

Arguments

`...`	an arbitrary number of SQM objects. Alternatively, a single list containing an arbitrary number of SQM objects.
`tax_source`	character. Features used for calculating aggregated abundances at the different taxonomic ranks. Either `"orfs"` or `"contigs"` (default `"orfs"`). If the objects being combined contain a subset of taxa or bins, this parameter can be set to `TRUE`.
`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 (default `TRUE`).
`rescale_copy_number`	logical. If `TRUE`, copy numbers with be recalculated using the RecA/RadA coverages in the subset. Otherwise, RecA/RadA coverages will be taken from the parent object with the highest RecA/RadA coverages. By default it is set to `TRUE`, which means that the returned copy numbers will represent the average copy number per function in the genomes of the selected bins or contigs. If any SQM objects that are being combined contain a functional subset rather than a contig/bins subset, this parameter should be set to `FALSE`.
`recalculate_bin_stats`	logical. If `TRUE`, bin stats and taxonomy are recalculated based on the contigs present in the subsetted object (default `TRUE`).

Value

A SQM or SQMbunch object

Examples

data(Hadza)
# Select Carbohydrate metabolism ORFs in Bacteroidota,
#  and Amino acid metabolism ORFs in Proteobacteria
bact = subsetTax(Hadza, "phylum", "Bacteroidota")
bact.carb = subsetFun(bact, "Carbohydrate metabolism")
baci = subsetTax(Hadza, "phylum", "Bacillota")
baci.amins = subsetFun(baci, "Amino acid metabolism")
bact.carb_proteo.amins = combineSQM(bact.carb, baci.amins, rescale_copy_number=FALSE)

SQMtools documentation built on April 3, 2025, 6:16 p.m.