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Transform OTU table values

Source: R/occurrences.R
mutate_occurrences_pq.Rd

Apply a transformation to all values in the OTU table. This is useful for computing relative abundances, log transformations, or other value-level operations.

The expression is evaluated vectorized across the entire OTU matrix with access to special variables (all as matrices matching OTU dimensions):

  • . = cell values (the OTU matrix)

  • sample_total = sum of each sample (repeated per column)

  • taxon_total = sum of each taxon (repeated per row)

  • sample_mean = mean of each sample (repeated per column)

  • taxon_mean = mean of each taxon (repeated per row)

  • sample_median = median of each sample (repeated per column)

  • taxon_median = median of each taxon (repeated per row)

Usage

mutate_occurrences_pq(physeq, expr)

Arguments

physeq

(phyloseq, required) A phyloseq object.

expr

An expression evaluated on the OTU matrix. The result replaces the original values. Use . to refer to cell values.

Value

A phyloseq object with transformed OTU values.

Author

Adrien Taudière

Examples

library(MiscMetabar)
# Convert to relative abundance (proportion of sample total)
mutate_occurrences_pq(data_fungi, . / sample_total)
#> 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 ]

# Log transformation (adding pseudocount)
mutate_occurrences_pq(data_fungi, log1p(.))
#> 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 ]

# Center by taxon mean
mutate_occurrences_pq(data_fungi, . - taxon_mean)
#> 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 ]