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Filter taxa of a phyloseq object based on the minimum number of sequences/samples

Source: R/dada_phyloseq.R
filt_taxa_pq.Rd

lifecycle-experimental

Basically a wraper of subset_taxa_pq().

Usage

filt_taxa_pq(
  physeq,
  min_nb_seq = NULL,
  min_occurence = NULL,
  combination = "AND",
  clean_pq = TRUE
)

Arguments

physeq

(required): a phyloseq-class object obtained using the phyloseq package.

min_nb_seq

(int default NULL) minimum number of sequences by taxa.

min_occurence

(int default NULL) minimum number of sample by taxa.

combination

Either "AND" (default) or "OR". If set to "AND" and both min_nb_seq and min_occurence are not NULL, the taxa must match the two condition to passe the filter. If set to "OR", taxa matching only one condition are kept.

clean_pq

(logical) If set to TRUE, empty samples and empty taxa (ASV, OTU) are discarded after filtering.

Value

a new phyloseq object

Author

Adrien Taudière

Examples

filt_taxa_pq(data_fungi, min_nb_seq = 20)
#> Cleaning suppress 0 taxa (  ) and 0 sample(s) (  ).
#> Number of non-matching ASV 0
#> Number of matching ASV 1420
#> Number of filtered-out ASV 32
#> Number of kept ASV 1388
#> Number of kept samples 185
#> Cleaning suppress 0 taxa and 0 samples.
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 1388 taxa and 185 samples ]
#> sample_data() Sample Data:       [ 185 samples by 7 sample variables ]
#> tax_table()   Taxonomy Table:    [ 1388 taxa by 12 taxonomic ranks ]
#> refseq()      DNAStringSet:      [ 1388 reference sequences ]
filt_taxa_pq(data_fungi, min_occurence = 2)
#> Cleaning suppress 0 taxa (  ) and 0 sample(s) (  ).
#> Number of non-matching ASV 0
#> Number of matching ASV 1420
#> Number of filtered-out ASV 206
#> Number of kept ASV 1214
#> Number of kept samples 185
#> Cleaning suppress 0 taxa and 0 samples.
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 1214 taxa and 185 samples ]
#> sample_data() Sample Data:       [ 185 samples by 7 sample variables ]
#> tax_table()   Taxonomy Table:    [ 1214 taxa by 12 taxonomic ranks ]
#> refseq()      DNAStringSet:      [ 1214 reference sequences ]
filt_taxa_pq(data_fungi,
  min_occurence = 2,
  min_nb_seq = 10, clean_pq = FALSE
)
#> Cleaning suppress 0 taxa (  ) and 0 sample(s) (  ).
#> Number of non-matching ASV 0
#> Number of matching ASV 1420
#> Number of filtered-out ASV 333
#> Number of kept ASV 1087
#> Number of kept samples 185
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 1087 taxa and 185 samples ]
#> sample_data() Sample Data:       [ 185 samples by 7 sample variables ]
#> tax_table()   Taxonomy Table:    [ 1087 taxa by 12 taxonomic ranks ]
#> refseq()      DNAStringSet:      [ 1087 reference sequences ]
filt_taxa_pq(data_fungi,
  min_occurence = 2,
  min_nb_seq = 10,
  combination = "OR"
)
#> Cleaning suppress 0 taxa (  ) and 0 sample(s) (  ).
#> Number of non-matching ASV 0
#> Number of matching ASV 1420
#> Number of filtered-out ASV 0
#> Number of kept ASV 1420
#> Number of kept samples 185
#> Cleaning suppress 0 taxa and 0 samples.
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 1420 taxa and 185 samples ]
#> sample_data() Sample Data:       [ 185 samples by 7 sample variables ]
#> tax_table()   Taxonomy Table:    [ 1420 taxa by 12 taxonomic ranks ]
#> refseq()      DNAStringSet:      [ 1420 reference sequences ]