Package index

Sample-scale verbs

Filter, select, mutate, slice, arrange, and rename samples.

filter_samples_pq()

Filter samples in a phyloseq object

select_samdata_pq()

Select columns from sample_data in a phyloseq object

mutate_samdata_pq()

Add or modify columns in sample_data

slice_samples_pq()

Subset samples by position

arrange_samples_pq()

Arrange samples by column values

rename_samples_pq()

Rename columns in sample_data

Taxa-scale verbs

Filter, select, mutate, slice, arrange, and rename taxa.

filter_taxa_pq()

Filter taxa in a phyloseq object

select_taxa_pq()

Select columns from tax_table in a phyloseq object

mutate_taxa_pq()

Add or modify columns in tax_table

slice_taxa_pq()

Subset taxa by position

arrange_taxa_pq()

Arrange taxa by column values

rename_taxa_pq()

Rename columns in tax_table

Occurrence-scale verbs

Filter and transform OTU table values.

filter_occurrences_pq()

Filter occurrences in the OTU table

mutate_occurrences_pq()

Transform OTU table values

Tree-scale verbs

Filter phylogenetic trees.

filter_tree_pq()

Filter phyloseq by tree topology

Helpers

Utility functions for common operations.

taxa_prevalence()

Calculate taxa prevalence

Decontamination

Remove contaminants using negative controls or control taxa.

decontam_sam_control()

Decontaminate based on negative/blank control samples

decontam_taxa_control()

Decontaminate based on control taxa

Chimera detection

Detect and benchmark chimeric sequences.

chimera_removal_dada2()

Remove chimeric sequences using dada2

chimera_removal_vs_ref()

Remove chimeric sequences using vsearch and a reference database

create_chimera_pq()

Create a phyloseq object with synthetic chimeric sequences

Contaminant detection & negative controls

Flag, classify and diagnose contaminant taxa.

contam_blocklist_pq()

Flag taxa whose genus belongs to a known-contaminant blocklist

contam_corr_pq()

Detect contaminants by correlating taxon reads with total sample depth

known_contaminant_genera()

Known reagent- and laboratory-contaminant genera

neg_control_classify_pq()

Classify taxa found in negative controls into contamination categories

neg_control_diag_pq()

Diagnose contamination from negative controls

neg_control_clean_pq()

Remove negative-control contaminants from a phyloseq object