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Detect contaminants from negative-control occurrence patterns

Source: R/identify_contam_negcontrol.R
identify_contam_negcontrol_pq.Rd

lifecycle-experimental

Examines taxa detected in negative-control samples and assigns each a contamination sub-type from read abundance and occurrence patterns:

  • artifact: very low total reads AND present in very few samples – likely sequencing noise or cross-talk.

  • lab_contaminant: predominantly found in negative controls relative to real samples – likely introduced during library preparation.

  • sample_contaminant: detected in controls but also widespread in real samples – may represent genuine biological signal.

This is a pure detector: it flags taxa and returns a contam_tbl without modifying physeq. Because sample_contaminant may be genuine signal, only artifact and lab_contaminant are flagged by default (see flag_categories). Use filter_contam_pq() to remove the flagged taxa.

Usage

identify_contam_negcontrol_pq(
  physeq,
  neg_control,
  min_reads_artifact = 10,
  max_samples_artifact = 2,
  max_ratio_lab_contam = 0.2,
  min_neg_samples_lab = 2,
  flag_categories = c("artifact", "lab_contaminant"),
  verbose = TRUE
)

Arguments

physeq

(phyloseq, required) A phyloseq object.

neg_control

An expression evaluated on sample_data returning TRUE for negative-control samples (e.g. is_control == TRUE). Use . to refer to the phyloseq object.

min_reads_artifact

(numeric, default 10) Maximum total reads for a taxon to be considered an artifact.

max_samples_artifact

(integer, default 2) Maximum total number of samples in which an artifact taxon may appear.

max_ratio_lab_contam

(numeric, default 0.2) Maximum ratio of non-control to control sample occurrences for the lab-contaminant category.

min_neg_samples_lab

(integer, default 2) Minimum number of control samples a lab-contaminant taxon must appear in.

flag_categories

(character, default c("artifact", "lab_contaminant")) Which sub-types to include in the returned contam_tbl. Add "sample_contaminant" to flag those as well.

verbose

(logical, default TRUE) Print a one-line detection summary.

Value

A contam_tbl with one row per flagged taxon, method = "negcontrol", and the evidence columns subtype (artifact, lab_contaminant, or sample_contaminant), total_reads, reads_in_neg, reads_in_samples, n_neg_samples, n_non_neg_samples, and ratio_non_neg_to_neg. Empty when no eligible taxon is found.

See also

filter_contam_pq() to remove flagged taxa.

Author

Adrien Taudière

Examples

library(MiscMetabar)
data(data_fungi)
# \donttest{
pq <- mutate_samdata_pq(
  data_fungi,
  is_control = sample_sums(.) < sort(sample_sums(.))[4]
)
flagged <- identify_contam_negcontrol_pq(pq, is_control)
#> ℹ negcontrol: flagged 0 taxa (artifact=0, lab_contaminant=0).
flagged
#> ✔ contam_tbl: no flagged taxa.
#> # A tibble: 0 × 9
#> # ℹ 9 variables: taxon <chr>, method <chr>, subtype <chr>, total_reads <dbl>,
#> #   reads_in_neg <dbl>, reads_in_samples <dbl>, n_neg_samples <dbl>,
#> #   n_non_neg_samples <dbl>, ratio_non_neg_to_neg <dbl>
# }